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- PDB-4uwo: Native di-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumonia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uwo | |||||||||
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Title | Native di-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumoniae has implications for drug binding. | |||||||||
![]() | METALLO-BETA-LACTAMASE VIM-26 | |||||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE / KLEBSIELLA PNEUMONIAE / DRUG BINDING SITE | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leiros, H.-K.S. / Edvardsen, K.S.W. / Bjerga, G.E.K. / Samuelsen, O. | |||||||||
![]() | ![]() Title: Structural and Biochemical Characterization of Vim-26 Show that Leu224 Has Implications for the Substrate Specificity of Vim Metallo-Beta-Lactamases. Authors: Leiros, H.S. / Edvardsen, K.S.W. / Bjerga, G.E.K. / 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 | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uwpC ![]() 4uwrC ![]() 4uwsC ![]() 2y8bS 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: 28074.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 9.5 Details: 21% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 5K, 0.1 M CHES BUFFER AT PH 9.5 0.1 M MAGNESIUM FORMATE, 4% GLYCEROL, 0.1 M MAGNESIUM FORMATE AND 4% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Sep 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 30529 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.87 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.9 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y8B Resolution: 1.555→21.967 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 18.61 / 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: 1.555→21.967 Å
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Refine LS restraints |
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LS refinement shell |
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