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Yorodumi- PDB-7dz0: Crystal structure of VIM-2 MBL in complex with 1-(but-3-en-1-yl)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dz0 | ||||||||||||
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Title | Crystal structure of VIM-2 MBL in complex with 1-(but-3-en-1-yl)-5-methyl-1H-imidazole-2-carboxylic acid | ||||||||||||
Components | Beta-lactamase class B VIM-2 | ||||||||||||
Keywords | HYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2 | ||||||||||||
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: 3.227 Å | ||||||||||||
Authors | Yan, Y.-H. / Li, G.-B. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-beta-lactamase inhibitors. Authors: Yan, Y.H. / Li, W. / Chen, W. / Li, C. / Zhu, K.R. / Deng, J. / Dai, Q.Q. / Yang, L.L. / Wang, Z. / Li, G.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dz0.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dz0.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dz0 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dz0 | HTTPS FTP |
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-Related structure data
Related structure data | 7du1C 7dubC 7dueC 7duxC 7duyC 7duzC 7dv0C 7dv1C 7dyyC 7dyzC 7dz1C 5lcaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24679.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Pseudomonas aeruginosa / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.62 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jul 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.227→73.192 Å / Num. obs: 8675 / % possible obs: 98.1 % / Redundancy: 12.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.658 / Rpim(I) all: 0.19 / Rrim(I) all: 0.685 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3.227→3.283 Å / Rmerge(I) obs: 1.797 / Num. unique obs: 100 / CC1/2: 0.791 / Rpim(I) all: 0.505 / Rrim(I) all: 1.867 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LCA Resolution: 3.227→73.192 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.9 Å2 / Biso mean: 17.6853 Å2 / Biso min: 0.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.227→73.192 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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