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- PDB-2y87: Native VIM-7. Structural and computational investigations of VIM-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y87 | ||||||
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Title | Native VIM-7. Structural and computational investigations of VIM-7: Insights into the substrate specificity of VIM metallo-beta- lactamases | ||||||
![]() | METALLO-B-LACTAMASE | ||||||
![]() | HYDROLASE / CEPHALOSPORINS / ANTIBIOTIC RECOGNITION | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saradhi, P. / Leiros, H.-K.S. / Ahmad, R. / Spencer, J. / Leiros, I. / Walsh, T.R. / Sundsfjord, A. / Samuelsen, O. | ||||||
![]() | ![]() Title: Structural and Computational Investigations of Vim- 7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases Authors: Saradhi, P. / Leiros, H.-K.S. / Ahmad, R. / Spencer, J. / Leiros, I. / Walsh, T.R. / Sundsfjord, A. / Samuelsen, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
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Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y8aC ![]() 2y8bC ![]() 1ko3S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 28141.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-UNX / | #5: Water | ChemComp-HOH / | Nonpolymer details | MICROHETEROGENEITY OBSERVED BETWEEN SULPHUR OF UNX A1296 AND HOH A2000. THE AUTHOR SUGGESTS THE ...MICROHETER | Sequence details | AUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE IS NUMBERED ACCORDING TO THE BBL ...AUTHOR DEFINED DISCONTINU | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 5 Details: 22.5-23.5% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 2K, 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 5.0, 8 MM BETA-MERCAPTOETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→29 Å / Num. obs: 19415 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 82.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KO3 Resolution: 1.86→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.606 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.396 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→20 Å
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Refine LS restraints |
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