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Yorodumi- PDB-2gmn: Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gmn | ||||||
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Title | Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum | ||||||
Components | Metallo-beta-lactamase | ||||||
Keywords | HYDROLASE / metallo-beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Calderone, V. / Benvenuti, M. / Stoczko, M. / Docquier, J.D. / Rossolini, G.M. / Mangani, S. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2006 Title: Postgenomic scan of metallo-beta-lactamase homologues in rhizobacteria: identification and characterization of BJP-1, a subclass B3 ortholog from Bradyrhizobium japonicum. Authors: Stoczko, M. / Frere, J.M. / Rossolini, G.M. / Docquier, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gmn.cif.gz | 229.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gmn.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gmn_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 2gmn_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 2gmn_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 2gmn_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gmn ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gmn | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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-Components
#1: Protein | Mass: 29937.283 Da / Num. of mol.: 2 / Fragment: residues 21-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Production host: Escherichia coli (E. coli) References: GenBank: 27381341, UniProt: Q89GW5*PLUS, beta-lactamase #2: Chemical | ChemComp-ZN / #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: 41.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 0.4M Na acetate, 40% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.281302 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2005 |
Radiation | Monochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.281302 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→38.576 Å / Num. obs: 87661 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.4→1.48 Å / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→38.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.319 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.075 / 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: 16.071 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→38.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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