+Open data
-Basic information
Entry | Database: PDB / ID: 3hbr | ||||||
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Title | Crystal structure of OXA-48 beta-lactamase | ||||||
Components | OXA-48 | ||||||
Keywords | HYDROLASE / CLASS D BETA-LACTAMASE / OXA-48 / ANTIBIOTIC / DIMER | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Calderone, V. / Mangani, S. / Benvenuti, M. / Rossolini, G.M. / Docquier, J.D. | ||||||
Citation | Journal: Chem.Biol. / Year: 2009 Title: Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases. Authors: Docquier, J.D. / Calderone, V. / De Luca, F. / Benvenuti, M. / Giuliani, F. / Bellucci, L. / Tafi, A. / Nordmann, P. / Botta, M. / Rossolini, G.M. / Mangani, S. #1: Journal: J.Am.Chem.Soc. / Year: 2000 Title: The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotics Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hbr.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hbr.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 3hbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hbr_validation.pdf.gz | 484.2 KB | Display | wwPDB validaton report |
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Full document | 3hbr_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 3hbr_validation.xml.gz | 49 KB | Display | |
Data in CIF | 3hbr_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hbr ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hbr | HTTPS FTP |
-Related structure data
Related structure data | 1k4fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30439.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 11978 / Gene: bla OXA-48 / Plasmid: pet9a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q6XEC0, beta-lactamase #2: Chemical | ChemComp-EDO / #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: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 10% PEG 4000, 8% 1-BUTANOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2005 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Laue geometry, 150 microns thin Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.514 Å / Num. all: 71756 / Num. obs: 71756 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.1004 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.9→1.949 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.176 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1K4F Resolution: 1.9→30.51 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.828 / SU B: 4.719 / SU ML: 0.143 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 16.906 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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