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- PDB-6i1h: Crystal structure of TP domain from Chlamydia trachomatis Penicil... -

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Basic information

Entry
Database: PDB / ID: 6i1h
TitleCrystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with meropenem
ComponentsPenicillin-binding protein,Penicillin-binding protein
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / membrane => GO:0016020
Similarity search - Function
Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-MER / Penicillin-binding protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with meropenem
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein,Penicillin-binding protein
B: Penicillin-binding protein,Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7074
Polymers72,9362
Non-polymers7712
Water3,207178
1
A: Penicillin-binding protein,Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8532
Polymers36,4681
Non-polymers3851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein,Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8532
Polymers36,4681
Non-polymers3851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.566, 112.566, 118.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Penicillin-binding protein,Penicillin-binding protein


Mass: 36467.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: pbp_2, ERS133248_00492 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E9FXJ8, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium citrate and 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→97.49 Å / Num. obs: 53168 / % possible obs: 93.8 % / Redundancy: 11.9 % / Rrim(I) all: 0.274 / Net I/σ(I): 10.7
Reflection shellResolution: 1.79→2.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
autoPROCdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZH

6hzh


Resolution: 1.78→97.49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.188 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25063 2579 4.9 %RANDOM
Rwork0.22134 ---
obs0.22271 50590 64.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.78→97.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5063 0 0 178 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025161
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9697045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42524.688192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57215799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2691524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.782→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 5 -
Rwork0.304 130 -
obs--2.24 %

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