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Yorodumi- PDB-4uwo: Native di-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumonia... -
+Open data
-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. | |||||||||
Components | METALLO-BETA-LACTAMASE VIM-26 | |||||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / KLEBSIELLA PNEUMONIAE / DRUG BINDING SITE | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding Similarity search - Function | |||||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 Å | |||||||||
Authors | Leiros, H.-K.S. / Edvardsen, K.S.W. / Bjerga, G.E.K. / Samuelsen, O. | |||||||||
Citation | Journal: FEBS J. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uwo.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwo.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uwo_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 4uwo_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 4uwo_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4uwo_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwo ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwo | HTTPS FTP |
-Related structure data
Related structure data | 4uwpC 4uwrC 4uwsC 2y8bS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E5BDC6 | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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