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Yorodumi- PDB-4v14: Structure and function analysis of MutT from the psychrofile fish... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v14 | |||||||||
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Title | Structure and function analysis of MutT from the psychrofile fish pathogen Aliivibrio salmonicida and the mesophile Vibrio cholerae | |||||||||
Components | MUTATOR MUTT PROTEIN | |||||||||
Keywords | HYDROLASE / VIBRIO CHOLERA MUTT | |||||||||
Function / homology | Function and homology information 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA repair Similarity search - Function | |||||||||
Biological species | VIBRIO CHOLERAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | |||||||||
Authors | Lian, K. / Leiros, H.-K.S. / Moe, E. | |||||||||
Citation | Journal: FEBS Open Bio / Year: 2015 Title: Mutt from the Fish Pathogen Aliivibrio Salmonicida is a Cold-Active Nucleotide-Pool Sanitization Enzyme with Unexpectedly High Thermostability. Authors: Lian, K. / Leiros, H.K. / Moe, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v14.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v14.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 4v14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v14 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v14 | HTTPS FTP |
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-Related structure data
Related structure data | 3a6vS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 15849.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Cell line (production host): AI CELLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A6XUL6, UniProt: Q9KPH6*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2 M LITHIUM SULPHATE, 0.1 M TRIS PH 8.5, 1.26 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Date: Mar 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→250 Å / Num. obs: 11909 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A6V Resolution: 2.42→10.001 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 31.46 / 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: 2.42→10.001 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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