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Open data
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Basic information
Entry | Database: PDB / ID: 4dk2 | ||||||
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Title | Crystal Structure of Open Trypanosoma brucei dUTPase | ||||||
![]() | Deoxyuridine triphosphatase | ||||||
![]() | HYDROLASE / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase / dUTP and Mg2+ binding | ||||||
Function / homology | ![]() dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
![]() | ![]() Title: On the catalytic mechanism of dimeric dUTPases. Authors: Hemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.7 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dk4C ![]() 4dkbC ![]() 4dl8C ![]() 4dlcC ![]() 1oglS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 33170.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 25% PEG1500, 0.1 M MMT buffer, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2011 |
Radiation | Monochromator: ACCEL fixed exit double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→42.05 Å / Num. all: 47254 / Num. obs: 47254 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6789 / Rsym value: 0.493 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OGL Resolution: 1.47→42.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.221 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.065 / ESU R Free: 0.07 / 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: 20.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→42.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.506 Å / Total num. of bins used: 20
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