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Yorodumi- PDB-2yf3: Crystal structure of DR2231, the MazG-like protein from Deinococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yf3 | |||||||||
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Title | Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, complex with manganese | |||||||||
Components | MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE | |||||||||
Keywords | HYDROLASE / DIMERIC DUTPASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Goncalves, A.M.D. / deSanctis, D. / McSweeney, S.M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans. Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yf3.cif.gz | 535.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yf3.ent.gz | 459 KB | Display | PDB format |
PDBx/mmJSON format | 2yf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/2yf3 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/2yf3 | HTTPS FTP |
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-Related structure data
Related structure data | 2yeuSC 2yf4C 2yf9C 2yfcC 2yfdC 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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Unit cell |
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-Components
#1: Protein | Mass: 16708.691 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 2.84 Å3/Da / Density % sol: 56.03 % / Description: NONE |
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Crystal grow | Details: 0.01M MAGNESIUM CHLORIDE, 0.05M SODIUM CACODYLATE, PH 6.0, 1M LITHIUM SULFATE. OVERNIGHT SOAK IN 250MM LITHIUM SULFATE / 750MM MANGANESE SULFATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2009 / Details: PT COATED MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 86122 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 19.167 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YEU Resolution: 2→43.12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.522 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.152 / 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: 25.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.12 Å
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