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Open data
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Basic information
Entry | Database: PDB / ID: 7bpd | ||||||
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Title | Crystal structural analysis of Swine dUTPase | ||||||
![]() | Deoxyuridine triphosphatase | ||||||
![]() | HYDROLASE / SWINE / dUTPASE / sDUT | ||||||
Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, R. / Peng, G.Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structural analysis of swine dUTPase Authors: Liang, R. / Peng, G.Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.1 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hquS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18537.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 200mM NaI, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97835 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→51.9 Å / Num. obs: 35796 / % possible obs: 83 % / Redundancy: 5.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 0.968 / Net I/σ(I): 23.67 |
Reflection shell | Resolution: 2.04→2.08 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2 / Num. unique obs: 1301 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.378 / Rrim(I) all: 0.968 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HQU Resolution: 2.04→46.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.063 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.227 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.4 Å2 / Biso mean: 38.493 Å2 / Biso min: 0.94 Å2
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Refinement step | Cycle: final / Resolution: 2.04→46.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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