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Open data
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Basic information
Entry | Database: PDB / ID: 3c2t | ||||||
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Title | Evolution of chlorella virus dUTPase | ||||||
![]() | Deoxyuridine triphosphatase | ||||||
![]() | HYDROLASE / dUTPase Chlorella Virus | ||||||
Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yamanishi, M. / Homma, K. / Zhang, Y. / Etten, L.V.J. / Moriyama, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 14810.870 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET-23a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.95 % |
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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: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 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→33.42 Å / Num. all: 8112 / Num. obs: 7922 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3→3.19 Å / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.7251 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→33.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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