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- PDB-6j25: CTX-M-64 beta-lactamase mutant-S130T -

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Basic information

Entry
Database: PDB / ID: 6j25
TitleCTX-M-64 beta-lactamase mutant-S130T
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
DepositionDec 30, 2018Deposition 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3062
Polymers58,3062
Non-polymers00
Water11,061614
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-4 kcal/mol
Surface area20300 Å2
Unit cell
Length a, b, c (Å)45.250, 105.990, 47.970
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 29152.924 Da / Num. of mol.: 2 / Mutation: S130T
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.: 614 / 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: 33.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M HEPES pH 7.4 25% 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: 1.04→53.22 Å / Num. obs: 170268 / % possible obs: 80.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 1.04→1.07 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5twd

5twd


Resolution: 1.2→52.99 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.933 / SU B: 0.481 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19407 6736 5 %RANDOM
Rwork0.18169 ---
obs0.18231 129002 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.174 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.2→52.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 0 614 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193964
X-RAY DIFFRACTIONr_bond_other_d0.0020.023770
X-RAY DIFFRACTIONr_angle_refined_deg2.4181.9675390
X-RAY DIFFRACTIONr_angle_other_deg1.238738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89324.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26615664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2791530
X-RAY DIFFRACTIONr_chiral_restr0.1690.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214418
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
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_it1.2960.9042078
X-RAY DIFFRACTIONr_mcbond_other1.2390.9012077
X-RAY DIFFRACTIONr_mcangle_it1.7431.362588
X-RAY DIFFRACTIONr_mcangle_other1.7511.3612589
X-RAY DIFFRACTIONr_scbond_it2.4271.1431886
X-RAY DIFFRACTIONr_scbond_other2.4261.1441887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4311.6322801
X-RAY DIFFRACTIONr_long_range_B_refined4.35512.6894656
X-RAY DIFFRACTIONr_long_range_B_other4.09311.9394502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 499 -
Rwork0.214 9342 -
obs--96.4 %

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