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- PDB-6ity: CTX-M-64 sulbactam complex -

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Basic information

Entry
Database: PDB / ID: 6ity
TitleCTX-M-64 sulbactam complex
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
ACRYLIC ACID / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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
DepositionNov 26, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8926
Polymers58,2782
Non-polymers6154
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint1 kcal/mol
Surface area20180 Å2
Unit cell
Length a, b, c (Å)45.302, 106.394, 47.549
Angle α, β, γ (deg.)90.00, 100.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 29138.900 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-TSL / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM


Mass: 235.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO5S
#3: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES (pH 7.4) and 17.5% polyethylene glycol 10000

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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: 1.78→46.71 Å / Num. obs: 23098 / % possible obs: 94.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.6
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6117 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→46.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.482 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22291 1157 4.8 %RANDOM
Rwork0.16083 ---
obs0.16383 23098 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.178 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.04 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.14→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 40 304 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193992
X-RAY DIFFRACTIONr_bond_other_d0.0020.023782
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9765414
X-RAY DIFFRACTIONr_angle_other_deg1.0938752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58624.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5441530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02742
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_it1.4941.7772078
X-RAY DIFFRACTIONr_mcbond_other1.4861.7712073
X-RAY DIFFRACTIONr_mcangle_it2.3522.6482584
X-RAY DIFFRACTIONr_mcangle_other2.3542.6482583
X-RAY DIFFRACTIONr_scbond_it2.0922.0681914
X-RAY DIFFRACTIONr_scbond_other2.0872.0681914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2533.0162831
X-RAY DIFFRACTIONr_long_range_B_refined5.27522.8824573
X-RAY DIFFRACTIONr_long_range_B_other5.17922.6484512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 80 -
Rwork0.166 1678 -
obs--98.21 %

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