+Open data
-Basic information
Entry | Database: PDB / ID: 2ov5 | ||||||
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Title | Crystal structure of the KPC-2 carbapenemase | ||||||
Components | Carbapenemase | ||||||
Keywords | HYDROLASE / carbapenemase / beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Ke, W. / Bethel, C.R. / Thomson, J.M. / Bonomo, R.A. / van den Akker, F. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structure of KPC-2: Insights into Carbapenemase Activity in Class A beta-Lactamases. Authors: Ke, W. / Bethel, C.R. / Thomson, J.M. / Bonomo, R.A. / Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ov5.cif.gz | 160 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ov5.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 2ov5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ov5_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 2ov5_full_validation.pdf.gz | 474.1 KB | Display | |
Data in XML | 2ov5_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 2ov5_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/2ov5 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/2ov5 | HTTPS FTP |
-Related structure data
Related structure data | 1dy6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 27664.143 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2, blaKPC-2 / Plasmid: pBR322 / Species (production host): Escherichia coli Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) Strain (production host): DH10B References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 16% PEG6000, 0.1M bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection twin | Type: hemihedral / Operator: h,-h-k,-l / Fraction: 0.42 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 64107 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.3 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DY6-A Resolution: 1.85→29.061 Å / Cross valid method: R-free / σ(F): 2573 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 34.797 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.821 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.061 Å
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Refine LS restraints |
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Xplor file |
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