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Yorodumi- PDB-2whg: Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2whg | ||||||
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Title | Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa | ||||||
Components | VIM-4 METALLO-BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / ALPHA-BETA/BETA-ALPHA FOLD | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lassaux, P. / Traore, D.A.K. / Galleni, M. / Ferrer, J.L. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2011 Title: Biochemical and Structural Characterization of the Subclass B1 Metallo-{Beta}-Lactamase Vim-4. Authors: Lassaux, P. / Traore, D.A.K. / Loisel, E. / Favier, A. / Docquier, J.D. / Sohier, J.S. / Laurent, C. / Bebrone, C. / Frere, J.M. / Ferrer, J.L. / Galleni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2whg.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whg.ent.gz | 159.4 KB | Display | PDB format |
PDBx/mmJSON format | 2whg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2whg_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 2whg_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 2whg_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2whg_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whg ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whg | HTTPS FTP |
-Related structure data
Related structure data | 1ko3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24446.150 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: GENE BLAVIM-4 / Plasmid: PET9A-VIM-4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS (DE3) References: UniProt: Q70E11, UniProt: Q8KRJ3*PLUS, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 7, 2008 |
Radiation | 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→47.3 Å / Num. obs: 52283 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.59 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.92 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.59 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KO3 Resolution: 1.9→47.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.864 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.138 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.3 Å
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Refine LS restraints |
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