+Open data
-Basic information
Entry | Database: PDB / ID: 2xy3 | ||||||
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Title | Structure of the Bacillus subtilis prophage dUTPase with dUpNHpp | ||||||
Components | SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS | ||||||
Keywords | HYDROLASE / PHE-LID | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Garcia-Nafria, J. / Harkiolaki, M. / Persson, R. / Fogg, M.J. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and its Complexes with Two Nucleotides Authors: Garcia-Nafria, J. / Harkiolaki, M. / Persson, R. / Fogg, M.J. / 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 | 2xy3.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xy3.ent.gz | 135.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xy3 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xy3 | HTTPS FTP |
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-Related structure data
Related structure data | 2xx6SC 2y1tC 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: 16172.509 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): B834 / References: UniProt: O34919, dUTP diphosphatase #2: Chemical | ChemComp-DUP / #3: Chemical | #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: 2.44 Å3/Da / Density % sol: 49.72 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 3.4 M 1,6-HEXANEDIOL, 0.1 M TRIS PH 8.5, 0.2M MGCL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→69.6 Å / Num. obs: 31651 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.55 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XX6 (CHAIN A) Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.763 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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