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- PDB-7ovf: Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ovf | ||||||
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Title | Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in Complex with compound 8 (JMV-7207) | ||||||
![]() | Metallo-beta-lactamase VIM-2-like protein | ||||||
![]() | HYDROLASE / metallo-beta-Lactamase / VIM-2 / triazole-thione / inhibitor / zinc | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassone, G. / Benvenuti, M. / Verdirosa, F. / Sannio, F. / Marcoccia, F. / Docquier, J.D. / Pozzi, C. / Mangani, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.1 KB | Display | ![]() |
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PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.3 KB | Display | ![]() |
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Full document | ![]() | 742.5 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oveC ![]() 7ovhC ![]() 6sp7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-1TH / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 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: 1.88→55.57 Å / Num. obs: 15310 / % possible obs: 89.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.059 / Rrim(I) all: 0.118 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 7 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2087 / CC1/2: 0.712 / Rpim(I) all: 0.49 / Rrim(I) all: 0.953 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SP7 Resolution: 1.9→55.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.305 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.188 / 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: 94.6 Å2 / Biso mean: 32.67 Å2 / Biso min: 17.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2268 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→55.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.945 Å / Rfactor Rfree error: 0
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