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- PDB-5xhr: Crystal structure of P99 beta-lactamase in complex with a penicil... -

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Basic information

Entry
Database: PDB / ID: 5xhr
TitleCrystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PXH / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPan, X. / Zhao, Y.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Modified Penicillin Molecule with Carbapenem-Like Stereochemistry Specifically Inhibits Class C beta-Lactamases
Authors: Pan, X. / He, Y. / Chen, T. / Chan, K.F. / Zhao, Y.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9122
Polymers39,5681
Non-polymers3431
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14610 Å2
Unit cell
Length a, b, c (Å)61.160, 69.330, 76.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39568.055 Da / Num. of mol.: 1 / Fragment: UNP residues 21-381
Source method: isolated from a genetically manipulated source
Details: PNM / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: P05364, beta-lactamase
#2: Chemical ChemComp-PXH / (2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-1,3-thiazolidine-4-carboxylic acid


Mass: 343.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.91836 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 1.74→69.33 Å / Num. obs: 30924 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.292 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XX2

1xx2


Resolution: 1.8→69 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.116 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1559 5 %RANDOM
Rwork0.21181 ---
obs0.21289 29328 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 22 142 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192937
X-RAY DIFFRACTIONr_bond_other_d0.0010.022793
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9594026
X-RAY DIFFRACTIONr_angle_other_deg0.67636438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46824.569116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1641512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
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_it1.15211480
X-RAY DIFFRACTIONr_mcbond_other1.14911479
X-RAY DIFFRACTIONr_mcangle_it1.7531.4931864
X-RAY DIFFRACTIONr_mcangle_other1.7531.4931865
X-RAY DIFFRACTIONr_scbond_it2.4371.31456
X-RAY DIFFRACTIONr_scbond_other2.4371.3011457
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7771.8342162
X-RAY DIFFRACTIONr_long_range_B_refined4.6898.5923453
X-RAY DIFFRACTIONr_long_range_B_other4.6838.5393395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 120 -
Rwork0.238 2117 -
obs--99.03 %

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