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Yorodumi- PDB-4aoz: B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aoz | ||||||
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Title | B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121) | ||||||
Components | PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Timm, J. / Garcia-Nafria, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism Authors: Garcia-Nafria, J. / Timm, J. / Harrison, C. / Turkenburg, J.P. / 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 | 4aoz.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aoz.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 4aoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aoz_validation.pdf.gz | 482.6 KB | Display | wwPDB validaton report |
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Full document | 4aoz_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 4aoz_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4aoz_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/4aoz ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4aoz | HTTPS FTP |
-Related structure data
Related structure data | 4ao5C 4aooC 4apzC 4b0hC 2xcdS 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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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 16431.760 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O31801, dUTP diphosphatase |
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-Non-polymers , 6 types, 576 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: 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: 47.74 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.2M NACL, 0.1M NA ACETATE PH 5, 20% PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50.13 Å / Num. obs: 29682 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.4 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XCD Resolution: 2.05→56.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.731 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.119 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→56.54 Å
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Refine LS restraints |
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