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Open data
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Basic information
Entry | Database: PDB / ID: 8qky | ||||||
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Title | Bacteriophage T5 dUTPase | ||||||
![]() | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
![]() | HYDROLASE / bacteriophage / T5 / dUTPase / Deoxyuridine triphosphate nucleotidohydrolases / dUTP | ||||||
Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Dzhus, U.F. / Selikhanov, G.K. / Glukhov, A.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions. Authors: Glukhov, A. / Marchenkov, V. / Dzhus, U. / Krutilina, A. / Selikhanov, G. / Gabdulkhakov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.2 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qldC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16223.650 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.075 M TRIS hydrochloride, 1.5 M Ammonium sulfate, 25% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 35488 / % possible obs: 99.9 % / Redundancy: 12.76 % / Biso Wilson estimate: 35.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.91 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2637 / CC1/2: 0.71 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.76 Å
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Refine LS restraints |
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LS refinement shell |
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