+Open data
-Basic information
Entry | Database: PDB / ID: 7u70 | ||||||
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Title | Crystal Structure of CTX-M-14 with compound 2 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / beta-lactamase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-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 / molecular replacement / Resolution: 1.36 Å | ||||||
Authors | Akhtar, A. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Probing the binding hot spots of KPC-2 carbapenemase using reversible tetrazole-based inhibitors Authors: DeFrees, K. / Cambeis, E.M. / Chen, Y. / Renslo, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u70.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u70.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 7u70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u70_validation.pdf.gz | 998.3 KB | Display | wwPDB validaton report |
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Full document | 7u70_full_validation.pdf.gz | 1001.5 KB | Display | |
Data in XML | 7u70_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 7u70_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/7u70 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/7u70 | HTTPS FTP |
-Related structure data
Related structure data | 7u8sC 7u9bC 7ua7C 1yltS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28000.547 Da / Num. of mol.: 2 / Fragment: UNP residues 23-284 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0, 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: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.0 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→46.715 Å / Num. all: 92146 / Num. obs: 92146 / % possible obs: 97.2 % / Redundancy: 3.3 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Rsym value: 0.063 / Net I/av σ(I): 6.9 / Net I/σ(I): 11.4 / Num. measured all: 305381 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLT Resolution: 1.36→46.715 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.02 Å2 / Biso mean: 12.8037 Å2 / Biso min: 3.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.36→46.715 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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