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Open data
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Basic information
Entry | Database: PDB / ID: 5yd7 | ||||||
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Title | Crystal Structure OF VIM-2 Metallo-beta-lactamase | ||||||
![]() | Beta-lactamase class B VIM-2 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wachino, J. | ||||||
![]() | ![]() Title: Crystal Structure Of VIM-2 Metallo-beta-lactamase Authors: Wachino, 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 | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 82.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nq2S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 26142.004 Da / Num. of mol.: 2 / Fragment: UNP residues 21-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Magnesium formate dehydrate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55.25 Å / Num. obs: 44283 / % possible obs: 99.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.324 / Num. unique obs: 6436 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4nq2 Resolution: 1.7→55.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.226 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.95 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→55.25 Å
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Refine LS restraints |
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