+Open data
-Basic information
Entry | Database: PDB / ID: 3ca9 | ||||||
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Title | Evolution of chlorella virus dUTPase | ||||||
Components | Deoxyuridine triphosphatase | ||||||
Keywords | HYDROLASE / dUTPase Chlorella Virus | ||||||
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 | Paramecium bursaria Chlorella virus IL3A | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Yamanishi, M. / Homma, K. / Zhang, Y. / Etten, L.V.J. / Moriyama, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase. Authors: Homma, K. / Moriyama, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ca9.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ca9.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ca9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ca9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3ca9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ca9_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3ca9_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3ca9 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3ca9 | HTTPS FTP |
-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17539.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium bursaria Chlorella virus IL3A Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLys / References: UniProt: Q5I3E5, dUTP diphosphatase #2: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG1450, 5mM magnesium chloride, 50mM sodium phosphate, 50mM sodium chloride, 1% glycerol, 2mM dUDP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 8218 / Num. obs: 8200 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.58 / Num. unique all: 808 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3073620.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.9855 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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