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Yorodumi- PDB-7ove: Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ove | ||||||
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Title | Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in Complex with compound 10 (JMV-7210) | ||||||
Components | Metallo-beta-lactamase VIM-2-like protein | ||||||
Keywords | HYDROLASE / metallo-beta-Lactamase / VIM-2 / triazole-thione / inhibitor / zinc | ||||||
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: 1.92 Å | ||||||
Authors | Tassone, G. / Benvenuti, M. / Verdirosa, F. / Sannio, F. / Mangani, S. / Docquier, J.D. / Pozzi, C. / Marcoccia, F. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: 1,2,4-Triazole-3-thione compounds with a 4-ethyl alkyl/aryl sulfide substituent are broad-spectrum metallo-beta-lactamase inhibitors with re-sensitization activity. Authors: Legru, A. / Verdirosa, F. / Hernandez, J.F. / Tassone, G. / Sannio, F. / Benvenuti, M. / Conde, P.A. / Bossis, G. / Thomas, C.A. / Crowder, M.W. / Dillenberger, M. / Becker, K. / Pozzi, C. / ...Authors: Legru, A. / Verdirosa, F. / Hernandez, J.F. / Tassone, G. / Sannio, F. / Benvenuti, M. / Conde, P.A. / Bossis, G. / Thomas, C.A. / Crowder, M.W. / Dillenberger, M. / Becker, K. / Pozzi, C. / Mangani, S. / Docquier, J.D. / Gavara, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ove.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ove.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ove.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ove_validation.pdf.gz | 733 KB | Display | wwPDB validaton report |
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Full document | 7ove_full_validation.pdf.gz | 733.2 KB | Display | |
Data in XML | 7ove_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7ove_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/7ove ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ove | HTTPS FTP |
-Related structure data
Related structure data | 7ovfC 7ovhC 6sp7S 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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Unit cell |
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-Components
#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: pET9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M cacodilate (pH 6.5), 5 mM DTT , 0.2 M Na-acetate, 26% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 4, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979499 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→55.66 Å / Num. obs: 16503 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.073 / Rrim(I) all: 0.144 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2369 / CC1/2: 0.807 / Rpim(I) all: 0.41 / Rrim(I) all: 0.825 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SP7 Resolution: 1.92→51.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.748 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 80.5 Å2 / Biso mean: 27.943 Å2 / Biso min: 9.13 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 1.92→51.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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