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Yorodumi- PDB-6yrp: Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yrp | ||||||
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Title | Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with JMV-4690 (Cpd 31) | ||||||
Components | Metallo-beta-lactamase VIM-2-like protein | ||||||
Keywords | HYDROLASE / Metallo-beta-lactamase / triazole-thione inhibitor / antibiotic resistance / carbapenem-hydrolyzing beta-lactamase | ||||||
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: 1.95 Å | ||||||
Authors | Docquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: 4-Amino-1,2,4-triazole-3-thione-derived Schiff bases as metallo-beta-lactamase inhibitors. Authors: Gavara, L. / Sevaille, L. / De Luca, F. / Mercuri, P. / Bebrone, C. / Feller, G. / Legru, A. / Cerboni, G. / Tanfoni, S. / Baud, D. / Cutolo, G. / Bestgen, B. / Chelini, G. / Verdirosa, F. / ...Authors: Gavara, L. / Sevaille, L. / De Luca, F. / Mercuri, P. / Bebrone, C. / Feller, G. / Legru, A. / Cerboni, G. / Tanfoni, S. / Baud, D. / Cutolo, G. / Bestgen, B. / Chelini, G. / Verdirosa, F. / Sannio, F. / Pozzi, C. / Benvenuti, M. / Kwapien, K. / Fischer, M. / Becker, K. / Frere, J.M. / Mangani, S. / Gresh, N. / Berthomieu, D. / Galleni, M. / Docquier, J.D. / Hernandez, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yrp.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yrp.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yrp_validation.pdf.gz | 774.6 KB | Display | wwPDB validaton report |
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Full document | 6yrp_full_validation.pdf.gz | 779 KB | Display | |
Data in XML | 6yrp_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6yrp_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrp ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrp | 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25539.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM / Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9 |
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-Non-polymers , 6 types, 131 molecules
#2: Chemical | #3: Chemical | ChemComp-PJB / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.8 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→56.104 Å / Num. all: 14141 / Num. obs: 14141 / % possible obs: 89 % / Redundancy: 3.7 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.102 / Rsym value: 0.089 / Net I/av σ(I): 6.1 / Net I/σ(I): 10 / Num. measured all: 52194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KO3 Resolution: 1.95→34.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.235 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.184 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.86 Å2 / Biso mean: 21.723 Å2 / Biso min: 8.74 Å2
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Refinement step | Cycle: final / Resolution: 1.95→34.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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