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- PDB-7dz1: Crystal structure of VIM-2 MBL in complex with 1-benzyl-5-methyl-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dz1 | ||||||||||||
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Title | Crystal structure of VIM-2 MBL in complex with 1-benzyl-5-methyl-1H-imidazole-2-carboxylic acid | ||||||||||||
![]() | Beta-lactamase class B VIM-2 | ||||||||||||
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Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yan, Y.-H. / Li, G.-B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7du1C ![]() 7dubC ![]() 7dueC ![]() 7duxC ![]() 7duyC ![]() 7duzC ![]() 7dv0C ![]() 7dv1C ![]() 7dyyC ![]() 7dyzC ![]() 7dz0C ![]() 5lcaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
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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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 2.708→55.65 Å / Num. obs: 11329 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.946 / Rmerge(I) obs: 0.424 / Rpim(I) all: 0.176 / Rrim(I) all: 0.46 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.708→2.755 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 541 / CC1/2: 0.643 / Rpim(I) all: 0.47 / Rrim(I) all: 1.246 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5LCA Resolution: 2.708→55.65 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.42 / 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: 93.99 Å2 / Biso mean: 12.3819 Å2 / Biso min: 0.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.708→55.65 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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