+Open data
-Basic information
Entry | Database: PDB / ID: 2xx6 | ||||||
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Title | Structure of the Bacillus subtilis prophage dUTPase, YosS | ||||||
Components | SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS | ||||||
Keywords | HYDROLASE | ||||||
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: 1.74 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 | 2xx6.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xx6.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/2xx6 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xx6 | HTTPS FTP |
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-Related structure data
Related structure data | 2xy3C 2y1tC 1dutS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: O34919, dUTP diphosphatase #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: 2.19 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1M IMIDAZOLEMALATE BUFFER PH 5.5, 30% (V/V) PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→88.99 Å / Num. obs: 52906 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.76→1.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DUT Resolution: 1.74→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.263 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARG61 FROM CHAIN B SHOWS BOND ANGLES OUT OF THE RANGE BUT ELECTRON DENSITY IS CLEAR FOR THAT REGION AND GEOMETRY IS AS SEEN.
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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: 23.266 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→10 Å
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Refine LS restraints |
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