+Open data
-Basic information
Entry | Database: PDB / ID: 6j2o | ||||||
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Title | Crystal structure of CTX-M-64 clavulanic acid complex | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cheng, Q. / Chen, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j2o.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j2o.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 6j2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j2o_validation.pdf.gz | 934.7 KB | Display | wwPDB validaton report |
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Full document | 6j2o_full_validation.pdf.gz | 932.8 KB | Display | |
Data in XML | 6j2o_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 6j2o_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/6j2o ftp://data.pdbj.org/pub/pdb/validation_reports/j2/6j2o | HTTPS FTP |
-Related structure data
Related structure data | 5zb7C 6ityC 6j25C 6j2bC 6j2kC 5twdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: 0.1 M HEPES, pH7.4, 17.5% PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.56→1.64 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6092 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.84 Å2 / Biso mean: 18.442 Å2 / Biso min: 9.79 Å2
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Refinement step | Cycle: final / Resolution: 1.9→42.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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