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Unverified Commit fe0550bb authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Create bonds based on chem_comp_bond records (#4904) 

* Create bonds based on chem_comp_bond records

* Fixed a test that assumed bonds would be in a particular order
parent cfcf0dcd
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Showing with 1239 additions and 15 deletions
wrappers/python/openmm/app/pdbxfile.py
View file @ fe0550bb
...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2015-2023 Stanford University and the Authors. Portions copyright (c) 2015-2025 Stanford University and the Authors.
Authors: Peter Eastman Authors: Peter Eastman
Contributors: Jason Swails Contributors: Jason Swails
...@@ -33,15 +33,16 @@ from __future__ import division, absolute_import, print_function ...@@ -33,15 +33,16 @@ from __future__ import division, absolute_import, print_function
__author__ = "Peter Eastman" __author__ = "Peter Eastman"
__version__ = "2.0" __version__ = "2.0"
import sys
import math
from openmm import Vec3, Platform from openmm import Vec3, Platform
from datetime import date
from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
from openmm.app.internal.unitcell import computePeriodicBoxVectors, computeLengthsAndAngles from openmm.app.internal.unitcell import computePeriodicBoxVectors, computeLengthsAndAngles
from openmm.app import Topology, PDBFile from openmm.app import topology, Topology, PDBFile
from openmm.unit import nanometers, angstroms, is_quantity, norm, Quantity from openmm.unit import nanometers, angstroms, is_quantity, Quantity
from . import element as elem from . import element as elem
import sys
import math
from datetime import date
from collections import defaultdict
try: try:
import numpy import numpy
except: except:
...@@ -92,9 +93,10 @@ class PDBxFile(object): ...@@ -92,9 +93,10 @@ class PDBxFile(object):
resNameCol = atomData.getAttributeIndex('auth_comp_id') resNameCol = atomData.getAttributeIndex('auth_comp_id')
if resNameCol == -1: if resNameCol == -1:
resNameCol = atomData.getAttributeIndex('label_comp_id') resNameCol = atomData.getAttributeIndex('label_comp_id')
resIdCol = atomData.getAttributeIndex('label_seq_id')
resNumCol = atomData.getAttributeIndex('auth_seq_id') resNumCol = atomData.getAttributeIndex('auth_seq_id')
if resNumCol == -1: if resNumCol == -1:
resNumCol = atomData.getAttributeIndex('label_seq_id') resNumCol = resIdCol
resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code') resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
chainIdCol = atomData.getAttributeIndex('auth_asym_id') chainIdCol = atomData.getAttributeIndex('auth_asym_id')
if chainIdCol == -1: if chainIdCol == -1:
...@@ -123,7 +125,7 @@ class PDBxFile(object): ...@@ -123,7 +125,7 @@ class PDBxFile(object):
atomsInResidue = set() atomsInResidue = set()
models = [] models = []
for row in atomData.getRowList(): for row in atomData.getRowList():
atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol])) atomKey = ((row[resIdCol], row[chainIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol]) model = ('1' if modelCol == -1 else row[modelCol])
if model not in models: if model not in models:
models.append(model) models.append(model)
...@@ -189,7 +191,6 @@ class PDBxFile(object): ...@@ -189,7 +191,6 @@ class PDBxFile(object):
self._positions[i] = self._positions[i]*nanometers self._positions[i] = self._positions[i]*nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame. ## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0] self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None self._numpyPositions = None
# Record unit cell information, if present. # Record unit cell information, if present.
...@@ -228,6 +229,45 @@ class PDBxFile(object): ...@@ -228,6 +229,45 @@ class PDBxFile(object):
top.addBond(bond[0], bond[1]) top.addBond(bond[0], bond[1])
existingBonds.add(bond) existingBonds.add(bond)
# Add bonds based on chem_comp_bond records.
bondData = block.getObj('chem_comp_bond')
if bondData is not None:
# Load the bond definitions for residues.
resNameCol = bondData.getAttributeIndex('comp_id')
atom1Col = bondData.getAttributeIndex('atom_id_1')
atom2Col = bondData.getAttributeIndex('atom_id_2')
bondOrderCol = bondData.getAttributeIndex('value_order')
resBonds = defaultdict(list)
for row in bondData.getRowList():
bondOrder = None if bondOrderCol == -1 else row[bondOrderCol]
resBonds[row[resNameCol]].append((row[atom1Col], row[atom2Col], bondOrder))
# Create the bonds.
bondTypes = defaultdict(lambda: None, {
'sing': topology.Single,
'doub': topology.Double,
'trip': topology.Triple,
'arom': topology.Aromatic
})
bondOrders = defaultdict(lambda: None, {
'sing': 1,
'doub': 2,
'trip': 3
})
for res in self.topology.residues():
if res.name in resBonds:
atoms = {atom.name: atom for atom in res.atoms()}
for atom1, atom2, bondOrder in resBonds[res.name]:
if atom1 in atoms and atom2 in atoms:
self.topology.addBond(atoms[atom1], atoms[atom2], bondTypes[bondOrder], bondOrders[bondOrder])
# Add bonds for standard residues.
self.topology.createStandardBonds()
def getTopology(self): def getTopology(self):
"""Get the Topology of the model.""" """Get the Topology of the model."""
return self.topology return self.topology
......
wrappers/python/openmm/app/topology.py
View file @ fe0550bb
...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2018 Stanford University and the Authors. Portions copyright (c) 2012-2025 Stanford University and the Authors.
Authors: Peter Eastman Authors: Peter Eastman
Contributors: Contributors:
...@@ -307,6 +307,13 @@ class Topology(object): ...@@ -307,6 +307,13 @@ class Topology(object):
Topology.loadBondDefinitions(os.path.join(os.path.dirname(__file__), 'data', 'residues.xml')) Topology.loadBondDefinitions(os.path.join(os.path.dirname(__file__), 'data', 'residues.xml'))
Topology._hasLoadedStandardBonds = True Topology._hasLoadedStandardBonds = True
# Record the existing bonds to avoid adding duplicate ones.
existingBonds = set([(bond[0], bond[1]) for bond in self._bonds])
# Add the new bonds.
for chain in self._chains: for chain in self._chains:
# First build a map of atom names to atoms. # First build a map of atom names to atoms.
...@@ -342,7 +349,10 @@ class Topology(object): ...@@ -342,7 +349,10 @@ class Topology(object):
toResidue = i toResidue = i
toAtom = bond[1] toAtom = bond[1]
if fromAtom in atomMaps[fromResidue] and toAtom in atomMaps[toResidue]: if fromAtom in atomMaps[fromResidue] and toAtom in atomMaps[toResidue]:
self.addBond(atomMaps[fromResidue][fromAtom], atomMaps[toResidue][toAtom]) atom1 = atomMaps[fromResidue][fromAtom]
atom2 = atomMaps[toResidue][toAtom]
if (atom1, atom2) not in existingBonds and (atom2, atom1) not in existingBonds:
self.addBond(atom1, atom2)
def createDisulfideBonds(self, positions): def createDisulfideBonds(self, positions):
"""Identify disulfide bonds based on proximity and add them to the """Identify disulfide bonds based on proximity and add them to the
......
wrappers/python/tests/TestPdbReporter.py
View file @ fe0550bb
...@@ -280,13 +280,13 @@ class TestPDBxReporter(unittest.TestCase): ...@@ -280,13 +280,13 @@ class TestPDBxReporter(unittest.TestCase):
validpdb = pdb validpdb = pdb
testpdb = app.PDBxFile(filename) testpdb = app.PDBxFile(filename)
validBonds = list(validpdb.topology.bonds()) validBonds = set(tuple(sorted((bond[0].index, bond[1].index))) for bond in validpdb.topology.bonds())
testBonds = list(testpdb.topology.bonds()) testBonds = set(tuple(sorted((bond[0].index, bond[1].index))) for bond in testpdb.topology.bonds())
self.assertEqual(len(validBonds), len(testBonds)) self.assertEqual(len(validBonds), len(testBonds))
for validBond, testBond in zip(validBonds, testBonds): for bond in validBonds:
self.assertEqual(str(validBond), str(testBond)) self.assertTrue(bond in testBonds)
......
wrappers/python/tests/TestPdbxFile.py
View file @ fe0550bb
...@@ -144,6 +144,43 @@ class TestPdbxFile(unittest.TestCase): ...@@ -144,6 +144,43 @@ class TestPdbxFile(unittest.TestCase):
self.assertEqual(bond1[0].name, bond2[0].name) self.assertEqual(bond1[0].name, bond2[0].name)
self.assertEqual(bond1[1].name, bond2[1].name) self.assertEqual(bond1[1].name, bond2[1].name)
def testChemCompBonds(self):
"""Test creating bonds based on chem_comp_bond records."""
pdb = PDBxFile('systems/6mvz.cif')
def bondCount(res1, atom1, res2, atom2):
count = 0
for bond in pdb.topology.bonds():
if (res1 == bond[0].residue.index and atom1 == bond[0].name) or (res2 == bond[0].residue.index and atom2 == bond[0].name):
if (res1 == bond[1].residue.index and atom1 == bond[1].name) or (res2 == bond[1].residue.index and atom2 == bond[1].name):
count += 1
return count
# Check some bonds that ought to be present.
self.assertEqual(1, bondCount(0, 'N', 0, 'CA'))
self.assertEqual(1, bondCount(0, 'C', 1, 'N'))
self.assertEqual(1, bondCount(1, 'CA', 1, 'CB'))
self.assertEqual(1, bondCount(1, 'C', 2, 'N'))
self.assertEqual(1, bondCount(2, 'CB', 2, 'CG'))
self.assertEqual(1, bondCount(2, 'C', 3, 'N'))
self.assertEqual(1, bondCount(3, 'C', 3, 'OXT'))
self.assertEqual(1, bondCount(4, 'O', 4, 'C1'))
# Check the types and orders of a few bonds.
for bond in pdb.topology.bonds():
if (bond[0].name == 'C' and bond[1].name == 'O') or (bond[1].name == 'C' and bond[0].name == 'O'):
self.assertEqual(topology.Double, bond.type)
self.assertEqual(2, bond.order)
if (bond[0].name == 'N' or bond[1].name == 'N'):
if bond[0].residue == bond[1].residue:
self.assertEqual(topology.Single, bond.type)
self.assertEqual(1, bond.order)
else:
self.assertEqual(None, bond.type)
self.assertEqual(None, bond.order)
def testMultiChain(self): def testMultiChain(self):
"""Test reading and writing a file that includes multiple chains""" """Test reading and writing a file that includes multiple chains"""
cif_ori = PDBxFile('systems/multichain.pdbx') cif_ori = PDBxFile('systems/multichain.pdbx')
......
wrappers/python/tests/systems/6mvz.cif 0 → 100644
View file @ fe0550bb
data_6MVZ
#
_entry.id 6MVZ
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.397
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 6MVZ pdb_00006mvz 10.2210/pdb6mvz/pdb
WWPDB D_1000237716 ? ?
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2019-09-11
2 'Structure model' 1 1 2024-10-23
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Data collection'
2 2 'Structure model' 'Database references'
3 2 'Structure model' 'Structure summary'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 2 'Structure model' chem_comp_atom
2 2 'Structure model' chem_comp_bond
3 2 'Structure model' database_2
4 2 'Structure model' pdbx_entry_details
5 2 'Structure model' pdbx_modification_feature
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 2 'Structure model' '_database_2.pdbx_DOI'
2 2 'Structure model' '_database_2.pdbx_database_accession'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 6MVZ
_pdbx_database_status.recvd_initial_deposition_date 2018-10-29
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Cameron, A.J.' 1 0000-0003-0680-6921
'Harris, P.W.R.' 2 0000-0002-2579-4543
'Brimble, M.A.' 3 0000-0002-7086-4096
'Squire, C.J.' 4 0000-0001-9212-0461
#
_citation.abstract ?
_citation.abstract_id_CAS ?
_citation.book_id_ISBN ?
_citation.book_publisher ?
_citation.book_publisher_city ?
_citation.book_title ?
_citation.coordinate_linkage ?
_citation.country UK
_citation.database_id_Medline ?
_citation.details ?
_citation.id primary
_citation.journal_abbrev Org.Biomol.Chem.
_citation.journal_id_ASTM ?
_citation.journal_id_CSD ?
_citation.journal_id_ISSN 1477-0539
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume 17
_citation.language ?
_citation.page_first 3902
_citation.page_last 3913
_citation.title
'Investigations of the key macrolactamisation step in the synthesis of cyclic tetrapeptide pseudoxylallemycin A.'
_citation.year 2019
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1039/c9ob00227h
_citation.pdbx_database_id_PubMed 30941386
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Cameron, A.J.' 1 ?
primary 'Squire, C.J.' 2 ?
primary 'Gerenton, A.' 3 ?
primary 'Stubbing, L.A.' 4 ?
primary 'Harris, P.W.R.' 5 ?
primary 'Brimble, M.A.' 6 ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn 'Linear precursor of pseudoxylallemycin A' 566.730 1 ? ? ? ?
2 non-polymer syn 'trifluoroacetic acid' 114.023 1 ? ? ? ?
3 water nat water 18.015 1 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code '(MLE)F(MLE)F'
_entity_poly.pdbx_seq_one_letter_code_can LFLF
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 'trifluoroacetic acid' TFA
3 water HOH
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 MLE n
1 2 PHE n
1 3 MLE n
1 4 PHE n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num 1
_pdbx_entity_src_syn.pdbx_end_seq_num 4
_pdbx_entity_src_syn.organism_scientific Xylaria
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 37991
_pdbx_entity_src_syn.details ?
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
HOH non-polymer . WATER ? 'H2 O' 18.015
MLE 'L-peptide linking' n N-METHYLLEUCINE ? 'C7 H15 N O2' 145.199
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
TFA non-polymer . 'trifluoroacetic acid' ? 'C2 H F3 O2' 114.023
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 MLE 1 1001 1001 MLE MLE A . n
A 1 2 PHE 2 1002 1002 PHE PHE A . n
A 1 3 MLE 3 1003 1003 MLE MLE A . n
A 1 4 PHE 4 1004 1004 PHE PHE A . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 TFA 1 2001 2001 TFA TFA A .
C 3 HOH 1 3001 3001 HOH HOH A .
#
loop_
_software.citation_id
_software.classification
_software.compiler_name
_software.compiler_version
_software.contact_author
_software.contact_author_email
_software.date
_software.description
_software.dependencies
_software.hardware
_software.language
_software.location
_software.mods
_software.name
_software.os
_software.os_version
_software.type
_software.version
_software.pdbx_ordinal
? refinement ? ? ? ? ? ? ? ? ? ? ? SHELXL ? ? ? . 1
? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2
? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3
? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXS ? ? ? . 4
#
_cell.angle_alpha 90.00
_cell.angle_alpha_esd ?
_cell.angle_beta 90.00
_cell.angle_beta_esd ?
_cell.angle_gamma 90.00
_cell.angle_gamma_esd ?
_cell.entry_id 6MVZ
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 8.255
_cell.length_a_esd ?
_cell.length_b 19.173
_cell.length_b_esd ?
_cell.length_c 23.446
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB 4
_cell.reciprocal_angle_alpha ?
_cell.reciprocal_angle_beta ?
_cell.reciprocal_angle_gamma ?
_cell.reciprocal_angle_alpha_esd ?
_cell.reciprocal_angle_beta_esd ?
_cell.reciprocal_angle_gamma_esd ?
_cell.reciprocal_length_a ?
_cell.reciprocal_length_b ?
_cell.reciprocal_length_c ?
_cell.reciprocal_length_a_esd ?
_cell.reciprocal_length_b_esd ?
_cell.reciprocal_length_c_esd ?
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 6MVZ
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 19
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.pdbx_full_space_group_name_H-M ?
#
_exptl.absorpt_coefficient_mu ?
_exptl.absorpt_correction_T_max ?
_exptl.absorpt_correction_T_min ?
_exptl.absorpt_correction_type ?
_exptl.absorpt_process_details ?
_exptl.entry_id 6MVZ
_exptl.crystals_number 1
_exptl.details ?
_exptl.method 'X-RAY DIFFRACTION'
_exptl.method_details ?
#
_exptl_crystal.colour ?
_exptl_crystal.density_diffrn ?
_exptl_crystal.density_Matthews 1.64
_exptl_crystal.density_method ?
_exptl_crystal.density_percent_sol 24.86
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.id 1
_exptl_crystal.preparation ?
_exptl_crystal.size_max ?
_exptl_crystal.size_mid ?
_exptl_crystal.size_min ?
_exptl_crystal.size_rad ?
_exptl_crystal.colour_lustre ?
_exptl_crystal.colour_modifier ?
_exptl_crystal.colour_primary ?
_exptl_crystal.density_meas ?
_exptl_crystal.density_meas_esd ?
_exptl_crystal.density_meas_gt ?
_exptl_crystal.density_meas_lt ?
_exptl_crystal.density_meas_temp ?
_exptl_crystal.density_meas_temp_esd ?
_exptl_crystal.density_meas_temp_gt ?
_exptl_crystal.density_meas_temp_lt ?
_exptl_crystal.pdbx_crystal_image_url ?
_exptl_crystal.pdbx_crystal_image_format ?
_exptl_crystal.pdbx_mosaicity ?
_exptl_crystal.pdbx_mosaicity_esd ?
#
_exptl_crystal_grow.apparatus ?
_exptl_crystal_grow.atmosphere ?
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.details ?
_exptl_crystal_grow.method EVAPORATION
_exptl_crystal_grow.method_ref ?
_exptl_crystal_grow.pH ?
_exptl_crystal_grow.pressure ?
_exptl_crystal_grow.pressure_esd ?
_exptl_crystal_grow.seeding ?
_exptl_crystal_grow.seeding_ref ?
_exptl_crystal_grow.temp 293
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.temp_esd ?
_exptl_crystal_grow.time ?
_exptl_crystal_grow.pdbx_details 'ethanol, water'
_exptl_crystal_grow.pdbx_pH_range ?
#
_diffrn.ambient_environment ?
_diffrn.ambient_temp 100
_diffrn.ambient_temp_details ?
_diffrn.ambient_temp_esd ?
_diffrn.crystal_id 1
_diffrn.crystal_support ?
_diffrn.crystal_treatment ?
_diffrn.details ?
_diffrn.id 1
_diffrn.ambient_pressure ?
_diffrn.ambient_pressure_esd ?
_diffrn.ambient_pressure_gt ?
_diffrn.ambient_pressure_lt ?
_diffrn.ambient_temp_gt ?
_diffrn.ambient_temp_lt ?
_diffrn.pdbx_serial_crystal_experiment N
#
_diffrn_detector.details ?
_diffrn_detector.detector PIXEL
_diffrn_detector.diffrn_id 1
_diffrn_detector.type 'DECTRIS EIGER X 16M'
_diffrn_detector.area_resol_mean ?
_diffrn_detector.dtime ?
_diffrn_detector.pdbx_frames_total ?
_diffrn_detector.pdbx_collection_time_total ?
_diffrn_detector.pdbx_collection_date 2018-07-13
_diffrn_detector.pdbx_frequency ?
#
_diffrn_radiation.collimation ?
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.filter_edge ?
_diffrn_radiation.inhomogeneity ?
_diffrn_radiation.monochromator ?
_diffrn_radiation.polarisn_norm ?
_diffrn_radiation.polarisn_ratio ?
_diffrn_radiation.probe ?
_diffrn_radiation.type ?
_diffrn_radiation.xray_symbol ?
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.pdbx_wavelength_list ?
_diffrn_radiation.pdbx_wavelength ?
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_analyzer ?
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.71075
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.current ?
_diffrn_source.details ?
_diffrn_source.diffrn_id 1
_diffrn_source.power ?
_diffrn_source.size ?
_diffrn_source.source SYNCHROTRON
_diffrn_source.target ?
_diffrn_source.type 'AUSTRALIAN SYNCHROTRON BEAMLINE MX2'
_diffrn_source.voltage ?
_diffrn_source.take-off_angle ?
_diffrn_source.pdbx_wavelength_list 0.71075
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_synchrotron_beamline MX2
_diffrn_source.pdbx_synchrotron_site 'Australian Synchrotron'
#
_reflns.B_iso_Wilson_estimate ?
_reflns.entry_id 6MVZ
_reflns.data_reduction_details ?
_reflns.data_reduction_method ?
_reflns.d_resolution_high 0.83
_reflns.d_resolution_low 23.44
_reflns.details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.number_all ?
_reflns.number_obs 4332
_reflns.observed_criterion ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.observed_criterion_I_max ?
_reflns.observed_criterion_I_min ?
_reflns.observed_criterion_sigma_F ?
_reflns.observed_criterion_sigma_I ?
_reflns.percent_possible_obs 98.0
_reflns.R_free_details ?
_reflns.Rmerge_F_all ?
_reflns.Rmerge_F_obs ?
_reflns.Friedel_coverage ?
_reflns.number_gt ?
_reflns.threshold_expression ?
_reflns.pdbx_redundancy 14.3
_reflns.pdbx_Rmerge_I_obs 0.117
_reflns.pdbx_Rmerge_I_all ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_av_sigmaI ?
_reflns.pdbx_netI_over_sigmaI 22.9
_reflns.pdbx_res_netI_over_av_sigmaI_2 ?
_reflns.pdbx_res_netI_over_sigmaI_2 ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_d_res_high_opt ?
_reflns.pdbx_d_res_low_opt ?
_reflns.pdbx_d_res_opt_method ?
_reflns.phase_calculation_details ?
_reflns.pdbx_Rrim_I_all ?
_reflns.pdbx_Rpim_I_all 0.033
_reflns.pdbx_d_opt ?
_reflns.pdbx_number_measured_all ?
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.pdbx_CC_half 0.989
_reflns.pdbx_R_split ?
#
_reflns_shell.d_res_high 0.83
_reflns_shell.d_res_low 0.85
_reflns_shell.meanI_over_sigI_all ?
_reflns_shell.meanI_over_sigI_obs 16.5
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_possible ?
_reflns_shell.number_unique_all ?
_reflns_shell.number_unique_obs 253
_reflns_shell.percent_possible_all 83.8
_reflns_shell.percent_possible_obs ?
_reflns_shell.Rmerge_F_all ?
_reflns_shell.Rmerge_F_obs ?
_reflns_shell.Rmerge_I_all ?
_reflns_shell.Rmerge_I_obs 0.127
_reflns_shell.meanI_over_sigI_gt ?
_reflns_shell.meanI_over_uI_all ?
_reflns_shell.meanI_over_uI_gt ?
_reflns_shell.number_measured_gt ?
_reflns_shell.number_unique_gt ?
_reflns_shell.percent_possible_gt ?
_reflns_shell.Rmerge_F_gt ?
_reflns_shell.Rmerge_I_gt ?
_reflns_shell.pdbx_redundancy 11.9
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.pdbx_chi_squared ?
_reflns_shell.pdbx_netI_over_sigmaI_all ?
_reflns_shell.pdbx_netI_over_sigmaI_obs ?
_reflns_shell.pdbx_Rrim_I_all ?
_reflns_shell.pdbx_Rpim_I_all 0.038
_reflns_shell.pdbx_rejects ?
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
_reflns_shell.pdbx_CC_half 0.990
_reflns_shell.pdbx_R_split ?
#
_refine.aniso_B[1][1] ?
_refine.aniso_B[1][2] ?
_refine.aniso_B[1][3] ?
_refine.aniso_B[2][2] ?
_refine.aniso_B[2][3] ?
_refine.aniso_B[3][3] ?
_refine.B_iso_max ?
_refine.B_iso_mean ?
_refine.B_iso_min ?
_refine.correlation_coeff_Fo_to_Fc ?
_refine.correlation_coeff_Fo_to_Fc_free ?
_refine.details 'full least squares refinement using SHELXL, anisotropic atoms, riding hydrogens.'
_refine.diff_density_max ?
_refine.diff_density_max_esd ?
_refine.diff_density_min ?
_refine.diff_density_min_esd ?
_refine.diff_density_rms ?
_refine.diff_density_rms_esd ?
_refine.entry_id 6MVZ
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.ls_abs_structure_details ?
_refine.ls_abs_structure_Flack ?
_refine.ls_abs_structure_Flack_esd ?
_refine.ls_abs_structure_Rogers ?
_refine.ls_abs_structure_Rogers_esd ?
_refine.ls_d_res_high 0.83
_refine.ls_d_res_low 23.44
_refine.ls_extinction_coef ?
_refine.ls_extinction_coef_esd ?
_refine.ls_extinction_expression ?
_refine.ls_extinction_method ?
_refine.ls_goodness_of_fit_all ?
_refine.ls_goodness_of_fit_all_esd ?
_refine.ls_goodness_of_fit_obs ?
_refine.ls_goodness_of_fit_obs_esd ?
_refine.ls_hydrogen_treatment ?
_refine.ls_matrix_type ?
_refine.ls_number_constraints ?
_refine.ls_number_parameters ?
_refine.ls_number_reflns_all ?
_refine.ls_number_reflns_obs 4332
_refine.ls_number_reflns_R_free ?
_refine.ls_number_reflns_R_work ?
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 100
_refine.ls_percent_reflns_R_free ?
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs 0.0675
_refine.ls_R_factor_R_free ?
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work ?
_refine.ls_R_Fsqd_factor_obs ?
_refine.ls_R_I_factor_obs ?
_refine.ls_redundancy_reflns_all ?
_refine.ls_redundancy_reflns_obs ?
_refine.ls_restrained_S_all ?
_refine.ls_restrained_S_obs ?
_refine.ls_shift_over_esd_max ?
_refine.ls_shift_over_esd_mean ?
_refine.ls_structure_factor_coef ?
_refine.ls_weighting_details ?
_refine.ls_weighting_scheme ?
_refine.ls_wR_factor_all ?
_refine.ls_wR_factor_obs ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.occupancy_max ?
_refine.occupancy_min ?
_refine.solvent_model_details ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.ls_R_factor_gt ?
_refine.ls_goodness_of_fit_gt ?
_refine.ls_goodness_of_fit_ref ?
_refine.ls_shift_over_su_max ?
_refine.ls_shift_over_su_max_lt ?
_refine.ls_shift_over_su_mean ?
_refine.ls_shift_over_su_mean_lt ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F ?
_refine.pdbx_ls_sigma_Fsqd ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_ls_cross_valid_method NONE
_refine.pdbx_method_to_determine_struct 'AB INITIO PHASING'
_refine.pdbx_starting_model ?
_refine.pdbx_stereochemistry_target_values ?
_refine.pdbx_R_Free_selection_details ?
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_overall_ESU_R_Free ?
_refine.pdbx_solvent_vdw_probe_radii ?
_refine.pdbx_solvent_ion_probe_radii ?
_refine.pdbx_solvent_shrinkage_radii ?
_refine.pdbx_real_space_R ?
_refine.pdbx_density_correlation ?
_refine.pdbx_pd_number_of_powder_patterns ?
_refine.pdbx_pd_number_of_points ?
_refine.pdbx_pd_meas_number_of_points ?
_refine.pdbx_pd_proc_ls_prof_R_factor ?
_refine.pdbx_pd_proc_ls_prof_wR_factor ?
_refine.pdbx_pd_Marquardt_correlation_coeff ?
_refine.pdbx_pd_Fsqrd_R_factor ?
_refine.pdbx_pd_ls_matrix_band_width ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.pdbx_diffrn_id 1
_refine.overall_SU_B ?
_refine.overall_SU_ML ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_average_fsc_overall ?
_refine.pdbx_average_fsc_work ?
_refine.pdbx_average_fsc_free ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 41
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 7
_refine_hist.number_atoms_solvent 1
_refine_hist.number_atoms_total 49
_refine_hist.d_res_high 0.83
_refine_hist.d_res_low 23.44
#
_struct.entry_id 6MVZ
_struct.title 'Mle-Phe-Mle-Phe. Linear precursor of pseudoxylallemycin A.'
_struct.pdbx_model_details ?
_struct.pdbx_formula_weight ?
_struct.pdbx_formula_weight_method ?
_struct.pdbx_model_type_details ?
_struct.pdbx_CASP_flag N
#
_struct_keywords.entry_id 6MVZ
_struct_keywords.text 'tetrapeptide, N-methyl leucine, linear precursor of pseudoxylallemycin A, ANTIBIOTIC'
_struct_keywords.pdbx_keywords ANTIBIOTIC
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 6MVZ
_struct_ref.pdbx_db_accession 6MVZ
_struct_ref.pdbx_db_isoform ?
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin 1
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 6MVZ
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 1
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 4
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 6MVZ
_struct_ref_seq.db_align_beg 1001
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 1004
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 1001
_struct_ref_seq.pdbx_auth_seq_align_end 1004
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details monomeric
_pdbx_struct_assembly.oligomeric_count 1
#
loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1 'ABSA (A^2)' 0 ?
1 MORE 0 ?
1 'SSA (A^2)' 890 ?
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
_pdbx_struct_assembly_auth_evidence.id 1
_pdbx_struct_assembly_auth_evidence.assembly_id 1
_pdbx_struct_assembly_auth_evidence.experimental_support none
_pdbx_struct_assembly_auth_evidence.details ?
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale both ? A MLE 1 C ? ? ? 1_555 A PHE 2 N ? ? A MLE 1001 A PHE 1002 1_555 ? ? ? ? ? ? ? 1.332 ? ?
covale2 covale both ? A PHE 2 C ? ? ? 1_555 A MLE 3 N ? ? A PHE 1002 A MLE 1003 1_555 ? ? ? ? ? ? ? 1.336 ? ?
covale3 covale both ? A MLE 3 C ? ? ? 1_555 A PHE 4 N ? ? A MLE 1003 A PHE 1004 1_555 ? ? ? ? ? ? ? 1.356 ? ?
#
_struct_conn_type.id covale
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.label_alt_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.modified_residue_label_alt_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.symmetry
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.modified_residue_symmetry
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
1 MLE A 1 ? . . . . MLE A 1001 ? 1_555 . . . . . . . LEU 1 MLE Methylation 'Named protein modification'
2 MLE A 3 ? . . . . MLE A 1003 ? 1_555 . . . . . . . LEU 1 MLE Methylation 'Named protein modification'
#
_struct_site.id AC1
_struct_site.pdbx_evidence_code Software
_struct_site.pdbx_auth_asym_id A
_struct_site.pdbx_auth_comp_id TFA
_struct_site.pdbx_auth_seq_id 2001
_struct_site.pdbx_auth_ins_code ?
_struct_site.pdbx_num_residues 8
_struct_site.details 'binding site for residue TFA A 2001'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 8 MLE A 1 ? MLE A 1001 . ? 3_646 ?
2 AC1 8 MLE A 1 ? MLE A 1001 . ? 2_664 ?
3 AC1 8 PHE A 2 ? PHE A 1002 . ? 4_666 ?
4 AC1 8 MLE A 3 ? MLE A 1003 . ? 2_664 ?
5 AC1 8 MLE A 3 ? MLE A 1003 . ? 1_655 ?
6 AC1 8 PHE A 4 ? PHE A 1004 . ? 1_655 ?
7 AC1 8 PHE A 4 ? PHE A 1004 . ? 1_555 ?
8 AC1 8 HOH C . ? HOH A 3001 . ? 1_555 ?
#
_pdbx_entry_details.entry_id 6MVZ
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
_pdbx_entry_details.has_ligand_of_interest ?
_pdbx_entry_details.has_protein_modification Y
#
_pdbx_molecule_features.prd_id PRD_002335
_pdbx_molecule_features.name 'Linear precursor of pseudoxylallemycin A'
_pdbx_molecule_features.type Peptide-like
_pdbx_molecule_features.class Antibiotic
_pdbx_molecule_features.details
;Mle-Phe-Mle-Phe. Linear precursor of pseudoxylallemycin A. The peptide is linear, unlike Mle-Phe-Mle-Phe Pseudoxylallemycin A that is cyclic.
;
#
_pdbx_molecule.instance_id 1
_pdbx_molecule.prd_id PRD_002335
_pdbx_molecule.asym_id A
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
HOH O O N N 1
HOH H1 H N N 2
HOH H2 H N N 3
MLE N N N N 4
MLE CN C N N 5
MLE CA C N S 6
MLE CB C N N 7
MLE CG C N N 8
MLE CD1 C N N 9
MLE CD2 C N N 10
MLE C C N N 11
MLE O O N N 12
MLE OXT O N N 13
MLE H H N N 14
MLE HN1 H N N 15
MLE HN2 H N N 16
MLE HN3 H N N 17
MLE HA H N N 18
MLE HB2 H N N 19
MLE HB3 H N N 20
MLE HG H N N 21
MLE HD11 H N N 22
MLE HD12 H N N 23
MLE HD13 H N N 24
MLE HD21 H N N 25
MLE HD22 H N N 26
MLE HD23 H N N 27
MLE HXT H N N 28
PHE N N N N 29
PHE CA C N S 30
PHE C C N N 31
PHE O O N N 32
PHE CB C N N 33
PHE CG C Y N 34
PHE CD1 C Y N 35
PHE CD2 C Y N 36
PHE CE1 C Y N 37
PHE CE2 C Y N 38
PHE CZ C Y N 39
PHE OXT O N N 40
PHE H H N N 41
PHE H2 H N N 42
PHE HA H N N 43
PHE HB2 H N N 44
PHE HB3 H N N 45
PHE HD1 H N N 46
PHE HD2 H N N 47
PHE HE1 H N N 48
PHE HE2 H N N 49
PHE HZ H N N 50
PHE HXT H N N 51
TFA C1 C N N 52
TFA C2 C N N 53
TFA O O N N 54
TFA F1 F N N 55
TFA F2 F N N 56
TFA F3 F N N 57
TFA OXT O N N 58
TFA HXT H N N 59
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
HOH O H1 sing N N 1
HOH O H2 sing N N 2
MLE N CN sing N N 3
MLE N CA sing N N 4
MLE N H sing N N 5
MLE CN HN1 sing N N 6
MLE CN HN2 sing N N 7
MLE CN HN3 sing N N 8
MLE CA CB sing N N 9
MLE CA C sing N N 10
MLE CA HA sing N N 11
MLE CB CG sing N N 12
MLE CB HB2 sing N N 13
MLE CB HB3 sing N N 14
MLE CG CD1 sing N N 15
MLE CG CD2 sing N N 16
MLE CG HG sing N N 17
MLE CD1 HD11 sing N N 18
MLE CD1 HD12 sing N N 19
MLE CD1 HD13 sing N N 20
MLE CD2 HD21 sing N N 21
MLE CD2 HD22 sing N N 22
MLE CD2 HD23 sing N N 23
MLE C O doub N N 24
MLE C OXT sing N N 25
MLE OXT HXT sing N N 26
PHE N CA sing N N 27
PHE N H sing N N 28
PHE N H2 sing N N 29
PHE CA C sing N N 30
PHE CA CB sing N N 31
PHE CA HA sing N N 32
PHE C O doub N N 33
PHE C OXT sing N N 34
PHE CB CG sing N N 35
PHE CB HB2 sing N N 36
PHE CB HB3 sing N N 37
PHE CG CD1 doub Y N 38
PHE CG CD2 sing Y N 39
PHE CD1 CE1 sing Y N 40
PHE CD1 HD1 sing N N 41
PHE CD2 CE2 doub Y N 42
PHE CD2 HD2 sing N N 43
PHE CE1 CZ doub Y N 44
PHE CE1 HE1 sing N N 45
PHE CE2 CZ sing Y N 46
PHE CE2 HE2 sing N N 47
PHE CZ HZ sing N N 48
PHE OXT HXT sing N N 49
TFA C1 C2 sing N N 50
TFA C1 O doub N N 51
TFA C1 OXT sing N N 52
TFA C2 F1 sing N N 53
TFA C2 F2 sing N N 54
TFA C2 F3 sing N N 55
TFA OXT HXT sing N N 56
#
_atom_sites.entry_id 6MVZ
_atom_sites.fract_transf_matrix[1][1] 0.121139
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.052157
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.042651
_atom_sites.fract_transf_vector[1] 0.000000
_atom_sites.fract_transf_vector[2] 0.000000
_atom_sites.fract_transf_vector[3] 0.000000
#
loop_
_atom_type.symbol
C
F
N
O
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N . MLE A 1 1 ? -1.988 15.766 19.167 1.000 3.46 ? 1001 MLE A N 1
HETATM 2 C CN . MLE A 1 1 ? -1.911 16.924 18.234 1.000 4.02 ? 1001 MLE A CN 1
HETATM 3 C CA . MLE A 1 1 ? -0.663 15.233 19.589 1.000 3.44 ? 1001 MLE A CA 1
HETATM 4 C CB . MLE A 1 1 ? -0.898 14.158 20.669 1.000 3.83 ? 1001 MLE A CB 1
HETATM 5 C CG . MLE A 1 1 ? 0.374 13.573 21.288 1.000 4.10 ? 1001 MLE A CG 1
HETATM 6 C CD1 . MLE A 1 1 ? 1.110 14.593 22.142 1.000 5.16 ? 1001 MLE A CD1 1
HETATM 7 C CD2 . MLE A 1 1 ? 0.024 12.344 22.146 1.000 5.28 ? 1001 MLE A CD2 1
HETATM 8 C C . MLE A 1 1 ? 0.027 14.627 18.372 1.000 3.27 ? 1001 MLE A C 1
HETATM 9 O O . MLE A 1 1 ? -0.618 13.872 17.611 1.000 3.80 ? 1001 MLE A O 1
ATOM 10 N N . PHE A 1 2 ? 1.313 14.938 18.221 1.000 3.16 ? 1002 PHE A N 1
ATOM 11 C CA . PHE A 1 2 ? 2.117 14.450 17.105 1.000 3.40 ? 1002 PHE A CA 1
ATOM 12 C C . PHE A 1 2 ? 3.285 13.617 17.674 1.000 3.38 ? 1002 PHE A C 1
ATOM 13 O O . PHE A 1 2 ? 4.253 14.238 18.149 1.000 4.85 ? 1002 PHE A O 1
ATOM 14 C CB . PHE A 1 2 ? 2.706 15.619 16.292 1.000 4.09 ? 1002 PHE A CB 1
ATOM 15 C CG . PHE A 1 2 ? 1.665 16.560 15.713 1.000 3.75 ? 1002 PHE A CG 1
ATOM 16 C CD1 . PHE A 1 2 ? 1.127 16.338 14.447 1.000 4.01 ? 1002 PHE A CD1 1
ATOM 17 C CD2 . PHE A 1 2 ? 1.263 17.689 16.421 1.000 4.04 ? 1002 PHE A CD2 1
ATOM 18 C CE1 . PHE A 1 2 ? 0.208 17.235 13.901 1.000 4.10 ? 1002 PHE A CE1 1
ATOM 19 C CE2 . PHE A 1 2 ? 0.345 18.582 15.881 1.000 4.22 ? 1002 PHE A CE2 1
ATOM 20 C CZ . PHE A 1 2 ? -0.184 18.354 14.613 1.000 4.28 ? 1002 PHE A CZ 1
HETATM 21 N N . MLE A 1 3 ? 3.221 12.283 17.686 1.000 3.47 ? 1003 MLE A N 1
HETATM 22 C CN . MLE A 1 3 ? 2.107 11.519 17.092 1.000 4.27 ? 1003 MLE A CN 1
HETATM 23 C CA . MLE A 1 3 ? 4.402 11.518 18.168 1.000 3.56 ? 1003 MLE A CA 1
HETATM 24 C CB . MLE A 1 3 ? 4.091 10.495 19.268 1.000 4.09 ? 1003 MLE A CB 1
HETATM 25 C CG . MLE A 1 3 ? 4.714 10.855 20.618 1.000 4.27 ? 1003 MLE A CG 1
HETATM 26 C CD1 . MLE A 1 3 ? 4.659 9.698 21.604 1.000 4.99 ? 1003 MLE A CD1 1
HETATM 27 C CD2 . MLE A 1 3 ? 4.101 12.108 21.215 1.000 5.82 ? 1003 MLE A CD2 1
HETATM 28 C C . MLE A 1 3 ? 5.033 10.893 16.918 1.000 3.49 ? 1003 MLE A C 1
HETATM 29 O O . MLE A 1 3 ? 4.705 9.782 16.486 1.000 4.05 ? 1003 MLE A O 1
ATOM 30 N N . PHE A 1 4 ? 5.932 11.681 16.278 1.000 3.60 ? 1004 PHE A N 1
ATOM 31 C CA . PHE A 1 4 ? 6.466 11.344 14.967 1.000 3.73 ? 1004 PHE A CA 1
ATOM 32 C C . PHE A 1 4 ? 7.501 10.238 15.005 1.000 3.79 ? 1004 PHE A C 1
ATOM 33 O O . PHE A 1 4 ? 8.030 9.823 16.014 1.000 4.24 ? 1004 PHE A O 1
ATOM 34 C CB . PHE A 1 4 ? 7.087 12.596 14.319 1.000 4.08 ? 1004 PHE A CB 1
ATOM 35 C CG . PHE A 1 4 ? 6.070 13.618 13.854 1.000 3.84 ? 1004 PHE A CG 1
ATOM 36 C CD1 . PHE A 1 4 ? 5.165 13.316 12.849 1.000 4.80 ? 1004 PHE A CD1 1
ATOM 37 C CD2 . PHE A 1 4 ? 6.083 14.915 14.357 1.000 4.12 ? 1004 PHE A CD2 1
ATOM 38 C CE1 . PHE A 1 4 ? 4.280 14.266 12.363 1.000 5.01 ? 1004 PHE A CE1 1
ATOM 39 C CE2 . PHE A 1 4 ? 5.227 15.884 13.848 1.000 4.58 ? 1004 PHE A CE2 1
ATOM 40 C CZ . PHE A 1 4 ? 4.332 15.565 12.837 1.000 4.78 ? 1004 PHE A CZ 1
ATOM 41 O OXT . PHE A 1 4 ? 7.761 9.819 13.767 1.000 4.72 ? 1004 PHE A OXT 1
HETATM 42 C C1 . TFA B 2 . ? 10.847 8.106 13.529 1.000 3.89 ? 2001 TFA A C1 1
HETATM 43 C C2 . TFA B 2 . ? 11.368 9.443 12.938 1.000 4.30 ? 2001 TFA A C2 1
HETATM 44 O O . TFA B 2 . ? 9.614 8.001 13.619 1.000 4.59 ? 2001 TFA A O 1
HETATM 45 F F1 . TFA B 2 . ? 12.674 9.438 12.668 1.000 5.59 ? 2001 TFA A F1 1
HETATM 46 F F2 . TFA B 2 . ? 10.723 9.750 11.802 1.000 5.65 ? 2001 TFA A F2 1
HETATM 47 F F3 . TFA B 2 . ? 11.156 10.447 13.792 1.000 6.18 ? 2001 TFA A F3 1
HETATM 48 O OXT . TFA B 2 . ? 11.705 7.276 13.897 1.000 4.33 ? 2001 TFA A OXT 1
HETATM 49 O O . HOH C 3 . ? 14.071 7.413 15.349 1.000 4.53 ? 3001 HOH A O 1
#
loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.pdbx_label_alt_id
_atom_site_anisotrop.pdbx_label_comp_id
_atom_site_anisotrop.pdbx_label_asym_id
_atom_site_anisotrop.pdbx_label_seq_id
_atom_site_anisotrop.pdbx_PDB_ins_code
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.pdbx_auth_seq_id
_atom_site_anisotrop.pdbx_auth_comp_id
_atom_site_anisotrop.pdbx_auth_asym_id
_atom_site_anisotrop.pdbx_auth_atom_id
1 N N . MLE A 1 ? 0.0306 0.0436 0.0496 0.0007 -0.0034 -0.0040 1001 MLE A N
2 C CN . MLE A 1 ? 0.0403 0.0455 0.0577 0.0016 -0.0066 0.0005 1001 MLE A CN
3 C CA . MLE A 1 ? 0.0321 0.0432 0.0475 0.0020 -0.0031 -0.0032 1001 MLE A CA
4 C CB . MLE A 1 ? 0.0406 0.0453 0.0511 0.0002 0.0017 0.0010 1001 MLE A CB
5 C CG . MLE A 1 ? 0.0441 0.0534 0.0489 0.0044 -0.0022 0.0010 1001 MLE A CG
6 C CD1 . MLE A 1 ? 0.0601 0.0631 0.0613 -0.0043 -0.0156 0.0016 1001 MLE A CD1
7 C CD2 . MLE A 1 ? 0.0718 0.0553 0.0616 0.0054 -0.0042 0.0090 1001 MLE A CD2
8 C C . MLE A 1 ? 0.0319 0.0396 0.0455 0.0013 -0.0015 0.0003 1001 MLE A C
9 O O . MLE A 1 ? 0.0312 0.0525 0.0522 -0.0036 -0.0014 -0.0107 1001 MLE A O
10 N N . PHE A 2 ? 0.0274 0.0421 0.0434 0.0005 0.0009 -0.0029 1002 PHE A N
11 C CA . PHE A 2 ? 0.0295 0.0469 0.0450 0.0025 0.0000 -0.0059 1002 PHE A CA
12 C C . PHE A 2 ? 0.0265 0.0463 0.0481 0.0009 -0.0020 -0.0039 1002 PHE A C
13 O O . PHE A 2 ? 0.0382 0.0446 0.0905 0.0002 -0.0206 -0.0034 1002 PHE A O
14 C CB . PHE A 2 ? 0.0345 0.0567 0.0550 -0.0010 0.0032 0.0056 1002 PHE A CB
15 C CG . PHE A 2 ? 0.0309 0.0518 0.0514 -0.0033 0.0012 0.0068 1002 PHE A CG
16 C CD1 . PHE A 2 ? 0.0421 0.0521 0.0491 -0.0015 0.0022 -0.0006 1002 PHE A CD1
17 C CD2 . PHE A 2 ? 0.0452 0.0513 0.0478 -0.0038 -0.0030 0.0035 1002 PHE A CD2
18 C CE1 . PHE A 2 ? 0.0431 0.0549 0.0483 -0.0019 -0.0025 0.0039 1002 PHE A CE1
19 C CE2 . PHE A 2 ? 0.0532 0.0462 0.0512 -0.0019 0.0043 0.0006 1002 PHE A CE2
20 C CZ . PHE A 2 ? 0.0466 0.0492 0.0571 0.0012 -0.0031 0.0106 1002 PHE A CZ
21 N N . MLE A 3 ? 0.0243 0.0449 0.0547 -0.0003 -0.0028 -0.0049 1003 MLE A N
22 C CN . MLE A 3 ? 0.0375 0.0434 0.0716 -0.0030 -0.0064 -0.0039 1003 MLE A CN
23 C CA . MLE A 3 ? 0.0340 0.0447 0.0485 -0.0022 -0.0034 -0.0011 1003 MLE A CA
24 C CB . MLE A 3 ? 0.0451 0.0461 0.0549 -0.0017 -0.0006 0.0019 1003 MLE A CB
25 C CG . MLE A 3 ? 0.0458 0.0537 0.0532 -0.0022 0.0003 0.0011 1003 MLE A CG
26 C CD1 . MLE A 3 ? 0.0606 0.0586 0.0589 0.0051 0.0014 0.0048 1003 MLE A CD1
27 C CD2 . MLE A 3 ? 0.0897 0.0597 0.0587 0.0041 0.0060 -0.0071 1003 MLE A CD2
28 C C . MLE A 3 ? 0.0307 0.0393 0.0547 0.0018 0.0036 0.0034 1003 MLE A C
29 O O . MLE A 3 ? 0.0423 0.0429 0.0596 -0.0030 0.0025 -0.0051 1003 MLE A O
30 N N . PHE A 4 ? 0.0368 0.0433 0.0486 -0.0035 0.0026 -0.0030 1004 PHE A N
31 C CA . PHE A 4 ? 0.0360 0.0490 0.0483 0.0027 0.0002 -0.0034 1004 PHE A CA
32 C C . PHE A 4 ? 0.0378 0.0486 0.0490 -0.0018 0.0018 0.0018 1004 PHE A C
33 O O . PHE A 4 ? 0.0436 0.0540 0.0539 0.0009 -0.0041 0.0047 1004 PHE A O
34 C CB . PHE A 4 ? 0.0383 0.0546 0.0528 -0.0013 0.0039 0.0002 1004 PHE A CB
35 C CG . PHE A 4 ? 0.0385 0.0529 0.0459 -0.0007 0.0012 0.0042 1004 PHE A CG
36 C CD1 . PHE A 4 ? 0.0609 0.0548 0.0558 0.0029 -0.0077 -0.0063 1004 PHE A CD1
37 C CD2 . PHE A 4 ? 0.0418 0.0502 0.0552 -0.0060 0.0037 0.0025 1004 PHE A CD2
38 C CE1 . PHE A 4 ? 0.0590 0.0611 0.0590 0.0088 -0.0149 0.0014 1004 PHE A CE1
39 C CE2 . PHE A 4 ? 0.0483 0.0522 0.0632 0.0003 0.0048 0.0023 1004 PHE A CE2
40 C CZ . PHE A 4 ? 0.0521 0.0642 0.0546 0.0084 0.0037 0.0060 1004 PHE A CZ
41 O OXT . PHE A 4 ? 0.0569 0.0598 0.0518 0.0154 0.0021 0.0001 1004 PHE A OXT
42 C C1 . TFA B . ? 0.0397 0.0506 0.0488 -0.0001 0.0037 -0.0014 2001 TFA A C1
43 C C2 . TFA B . ? 0.0452 0.0571 0.0513 -0.0035 -0.0029 0.0006 2001 TFA A C2
44 O O . TFA B . ? 0.0372 0.0551 0.0717 0.0038 0.0053 0.0069 2001 TFA A O
45 F F1 . TFA B . ? 0.0494 0.0689 0.0814 -0.0098 0.0058 0.0072 2001 TFA A F1
46 F F2 . TFA B . ? 0.0677 0.0758 0.0583 -0.0099 -0.0082 0.0192 2001 TFA A F2
47 F F3 . TFA B . ? 0.0914 0.0531 0.0764 -0.0063 0.0072 -0.0110 2001 TFA A F3
48 O OXT . TFA B . ? 0.0397 0.0572 0.0577 0.0018 -0.0017 0.0055 2001 TFA A OXT
49 O O . HOH C . ? 0.0562 0.0433 0.0622 0.0062 -0.0090 -0.0037 3001 HOH A O
#
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