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- PDB-6j2o: Crystal structure of CTX-M-64 clavulanic acid complex -

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Basic information

Entry
Database: PDB / ID: 6j2o
TitleCrystal structure of CTX-M-64 clavulanic acid complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCheng, Q. / Chen, S.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Insight into the Mechanism of Inhibitor Resistance in CTX-M-199, a CTX-M-64 Variant Carrying the S130T Substitution.
Authors: Cheng, Q. / Xu, C. / Chai, J. / Zhang, R. / Wai Chi Chan, E. / Chen, S.
History
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.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 1.3May 21, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6454
Polymers61,3312
Non-polymers3142
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-3 kcal/mol
Surface area20120 Å2
Unit cell
Length a, b, c (Å)45.145, 105.726, 47.466
Angle α, β, γ (deg.)90.000, 100.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 30665.582 Da / Num. of mol.: 2 / Fragment: UNP residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-64, BK400_21830, pHNAH46_020
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C8CP57, beta-lactamase
#2: Chemical ChemComp-ISS / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal


Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.81 Å3/Da / Density % sol: 32.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1 M HEPES, pH7.4, 17.5% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.56→42.69 Å / Num. obs: 32311 / % possible obs: 91 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.4
Reflection shellResolution: 1.56→1.64 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6092

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TWD

5twd


Resolution: 1.9→42.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.142 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1670 4.9 %RANDOM
Rwork0.1573 ---
obs0.1594 32311 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.84 Å2 / Biso mean: 18.442 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å21.25 Å2
2---1.38 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.9→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 22 356 4274
Biso mean--34.36 29.26 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133974
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173780
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6575390
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5848760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1325514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39122.292192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19615662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7491530
X-RAY DIFFRACTIONr_chiral_restr0.080.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 98 -
Rwork0.161 2389 -
all-2487 -
obs--99.12 %

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