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Yorodumi- PDB-7pp0: Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pp0 | ||||||
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Title | Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 28 (JMV-7038) | ||||||
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: 1.73 Å | ||||||
Authors | Tassone, G. / Benvenuti, M. / Verdirosa, F. / Corsica, G. / Chelini, G. / De Luca, F. / Docquier, J.D. / Pozzi, C. / Mangani, S. | ||||||
Funding support | 1items
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Citation | Journal: Chemmedchem / Year: 2022 Title: 1,2,4-Triazole-3-Thione Analogues with a 2-Ethylbenzoic Acid at Position 4 as VIM-type Metallo-beta-Lactamase Inhibitors. Authors: Verdirosa, F. / Gavara, L. / Sevaille, L. / Tassone, G. / Corsica, G. / Legru, A. / Feller, G. / Chelini, G. / Mercuri, P.S. / Tanfoni, S. / Sannio, F. / Benvenuti, M. / Cerboni, G. / De ...Authors: Verdirosa, F. / Gavara, L. / Sevaille, L. / Tassone, G. / Corsica, G. / Legru, A. / Feller, G. / Chelini, G. / Mercuri, P.S. / Tanfoni, S. / Sannio, F. / Benvenuti, M. / Cerboni, G. / De Luca, F. / Bouajila, E. / Vo Hoang, Y. / Licznar-Fajardo, P. / Galleni, M. / Pozzi, C. / Mangani, S. / 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 | 7pp0.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pp0.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pp0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7pp0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7pp0_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7pp0_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/7pp0 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/7pp0 | HTTPS FTP |
-Related structure data
Related structure data | 6sp7S 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 on special symmetry positions |
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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-7ZN / | #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: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M cacodilate pH 6.5, 5mM DTT, 0.2M 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: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→55.76 Å / Num. obs: 22531 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.73→1.82 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3242 / CC1/2: 0.821 / Rpim(I) all: 0.337 / Rrim(I) all: 0.911 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SP7 Resolution: 1.73→55.76 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.915 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / 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: 66.73 Å2 / Biso mean: 26.637 Å2 / Biso min: 10.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.192 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→55.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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