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Yorodumi- PDB-2yb0: The Crystal Structure of Leishmania major dUTPase in complex deox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yb0 | ||||||
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Title | The Crystal Structure of Leishmania major dUTPase in complex deoxyuridine | ||||||
Components | DUTPASEDUTP diphosphatase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Hemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine. Authors: Hemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yb0.cif.gz | 417.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yb0.ent.gz | 347.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2yb0 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2yb0 | HTTPS FTP |
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-Related structure data
Related structure data | 2cicC 2cjeSC 2yayC 2yazC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30609.850 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: 252 / Plasmid: PET-YSBLLIC3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15826, dUTP diphosphatase #2: Chemical | ChemComp-DUR / #3: Chemical | ChemComp-SO4 / #4: 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: 4.29 Å3/Da / Density % sol: 71.32 % / Description: NONE |
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Crystal grow | Details: 0.1 M NACL, 0.1 M BIS-TRIS PH 6.5, 1.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→60.8 Å / Num. obs: 98557 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CJE Resolution: 2.28→54.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.849 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / 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: 85.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→54.59 Å
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Refine LS restraints |
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