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Yorodumi- PDB-2wrs: Crystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 f... -
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-Basic information
Entry | Database: PDB / ID: 2wrs | ||||||
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Title | Crystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa | ||||||
Components | BETA-LACTAMASE VIM-4 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Traore, D.A.K. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Gaumont, A.-C. / Frere, J.-M. ...Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Traore, D.A.K. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Gaumont, A.-C. / Frere, J.-M. / Ferrer, J.-L. / Hoffmann, K. / Galleni, M. / Bebrone, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-Beta-Lactamases. Authors: Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Kupper, M. / Frere, J.-M. / Hoffmann, K. / Galleni, M. / Bebrone, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wrs.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wrs.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/2wrs ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wrs | HTTPS FTP |
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-Related structure data
Related structure data | 3iofC 3iogC 2whgS 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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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) / Plasmid: PET9A-VIM-4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS (DE3) / References: UniProt: Q70E11, beta-lactamase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0 POWDER OF COMPOUND 18 IN THE DROP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 16118 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42.096 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.03 |
Reflection shell | Resolution: 2.79→2.96 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.43 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WHG Resolution: 2.79→43.27 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.864 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 38.177 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→43.27 Å
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