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- PDB-8hyd: Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-(2-(t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hyd | ||||||||||||
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Title | Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-(2-(thiophen-2-yl)ethyl)thiazole-4-carboxylic acid | ||||||||||||
![]() | Beta-lactamase class B VIM-2 | ||||||||||||
![]() | HYDROLASE / Beta-lactamase class B VIM-2 | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yan, Y.-H. / Zhu, K.-R. / Li, G.-B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding. Authors: Yan, Y.H. / Zhang, T.T. / Li, R. / Wang, S.Y. / Wei, L.L. / Wang, X.Y. / Zhu, K.R. / Li, S.R. / Liang, G.Q. / Yang, Z.B. / Yang, L.L. / Qin, S. / 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 | ![]() | 62.7 KB | Display | ![]() |
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PDB format | ![]() | 42.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 837.6 KB | Display | ![]() |
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Full document | ![]() | 839.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hx5C ![]() 8hxeC ![]() 8hxiC ![]() 8hxnC ![]() 8hxoC ![]() 8hxpC ![]() 8hxuC ![]() 8hxvC ![]() 8hxwC ![]() 8hy1C ![]() 8hy2C ![]() 8hy6C ![]() 8jaoC ![]() 7dv0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 24679.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2 Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-60J / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium Formate, 28%-35% (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: Oct 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→19.89 Å / Num. obs: 28787 / % possible obs: 95.68 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.71→1.77 Å / Num. unique obs: 2406 / CC1/2: 0.742 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DV0 Resolution: 1.71→19.551 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 21.54 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→19.551 Å
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Refine LS restraints |
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LS refinement shell |
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