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- PDB-4ua4: Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ua4 | ||||||
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Title | Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor | ||||||
![]() | Beta-lactamase class B VIM-2 | ||||||
![]() | HYDROLASE / Hydrolase Metallo-beta-Lactamase Complex | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor Authors: Spencer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.8 KB | Display | ![]() |
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PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.1 KB | Display | ![]() |
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Full document | ![]() | 472.2 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ko3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Bicine pH 9.0; 65 % 2-methyl-2,4-pentandiol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→29.64 Å / Num. obs: 115461 / % possible obs: 96.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KO3 Resolution: 1.25→67.68 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.209 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 16.888 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→67.68 Å
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Refine LS restraints |
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