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- PDB-5zb7: CTX-M-64 apoenzyme -

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Basic information

Entry
Database: PDB / ID: 5zb7
TitleCTX-M-64 apoenzyme
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / apoenzyme
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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
DepositionFeb 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3312
Polymers61,3312
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-2 kcal/mol
Surface area20270 Å2
Unit cell
Length a, b, c (Å)45.123, 106.898, 47.521
Angle α, β, γ (deg.)90.00, 99.80, 90.00
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C8CP57, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.0, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.44→53.45 Å / Num. obs: 78497 / % possible obs: 98.5 % / Redundancy: 5.1 % / Net I/σ(I): 12.262
Reflection shellResolution: 1.44→1.48 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5twd

5twd


Resolution: 1.63→46.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.297 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22775 2794 5.1 %RANDOM
Rwork0.19328 ---
obs0.19509 51465 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.08 Å2
2---0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.63→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 345 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193952
X-RAY DIFFRACTIONr_bond_other_d0.0020.023750
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9685368
X-RAY DIFFRACTIONr_angle_other_deg1.09338692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87324.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7081530
X-RAY DIFFRACTIONr_chiral_restr0.1240.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214404
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02730
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_it1.5721.4742074
X-RAY DIFFRACTIONr_mcbond_other1.571.4722073
X-RAY DIFFRACTIONr_mcangle_it2.1662.2032582
X-RAY DIFFRACTIONr_mcangle_other2.1672.2052583
X-RAY DIFFRACTIONr_scbond_it2.1361.721878
X-RAY DIFFRACTIONr_scbond_other2.1361.7221879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2082.4912787
X-RAY DIFFRACTIONr_long_range_B_refined4.60719.1644560
X-RAY DIFFRACTIONr_long_range_B_other4.48818.8154482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 189 -
Rwork0.241 3705 -
obs--95.61 %

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