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Yorodumi- PDB-7dyy: Crystal structure of VIM-2 MBL in complex with 1-((2-aminobenzo[d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dyy | ||||||||||||
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Title | Crystal structure of VIM-2 MBL in complex with 1-((2-aminobenzo[d]thiazol-6-yl)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: 1.798 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 | 7dyy.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dyy.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dyy_validation.pdf.gz | 994.4 KB | Display | wwPDB validaton report |
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Full document | 7dyy_full_validation.pdf.gz | 1003 KB | Display | |
Data in XML | 7dyy_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 7dyy_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dyy ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dyy | HTTPS FTP |
-Related structure data
Related structure data | 7du1C 7dubC 7dueC 7duxC 7duyC 7duzC 7dv0C 7dv1C 7dyzC 7dz0C 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: Chemical | #5: 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: 2.74 Å3/Da / Density % sol: 55.05 % |
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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: Oct 29, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.798→98.03 Å / Num. obs: 26848 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.482 / Rpim(I) all: 0.221 / Rrim(I) all: 0.532 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LCA Resolution: 1.798→51.841 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.35 / 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: 88.34 Å2 / Biso mean: 29.013 Å2 / Biso min: 10.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.798→51.841 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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