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Yorodumi- PDB-5njw: Crystal Structure of BJP-1 metallo beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5njw | ||||||
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Title | Crystal Structure of BJP-1 metallo beta-lactamase in complex with boric acid | ||||||
Components | Blr6230 protein | ||||||
Keywords | HYDROLASE / MBLs / BJP-1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bradyrhizobium diazoefficiens USDA 110 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S. | ||||||
Citation | Journal: Inorg.Chim.Acta. / Year: 2017 Title: Boric acid and acetate anion binding to subclass B3 metallo-Beta-lactamase BJP-1 provides clues for mechanism of action and inhibitor design Authors: Di Pisa, F. / Pozzi, C. / Benvenuti, M. / Docquier, J.-D. / De Luca, F. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5njw.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5njw.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 5njw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5njw_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 5njw_full_validation.pdf.gz | 475.5 KB | Display | |
Data in XML | 5njw_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 5njw_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/5njw ftp://data.pdbj.org/pub/pdb/validation_reports/nj/5njw | HTTPS FTP |
-Related structure data
Related structure data | 5nggC 3lvzS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31982.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria) Gene: blr6230 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89GW5 |
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-Non-polymers , 6 types, 589 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: 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: 2.07 Å3/Da / Density % sol: 40.57 % / Description: parallelepiped-shaped crystals |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium Suplhate, 30-35 % PEG400, 0.5 M sodium acetate, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→32.14 Å / Num. obs: 126849 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 5.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 120271 / CC1/2: 0.976 / % possible all: 95.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LVZ Resolution: 1.25→32.14 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.276 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.645 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→32.14 Å
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Refine LS restraints |
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