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- PDB-4dl8: Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dl8 | ||||||
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Title | Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+ | ||||||
![]() | Deoxyuridine triphosphatase | ||||||
![]() | HYDROLASE / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase | ||||||
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 | ![]() | 67.2 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 754.4 KB | Display | ![]() |
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Full document | ![]() | 754.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dk2C ![]() 4dk4C ![]() 4dkbSC ![]() 4dlcC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32204.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 172 molecules ![](data/chem/img/UMP.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AF3.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UMP / | ||||
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#3: Chemical | ChemComp-AF3 / | ||||
#4: Chemical | ChemComp-PO4 / | ||||
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.698→28.203 Å / Num. all: 33398 / Num. obs: 33398 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 23.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: REFINED 4DKB Starting model: PDB ENTRY 4DKB Resolution: 1.698→28.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1759 / WRfactor Rwork: 0.1545 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8909 / SU B: 1.681 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0828 / SU Rfree: 0.0837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / 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 max: 424.2 Å2 / Biso mean: 25.9297 Å2 / Biso min: 8.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.698→28.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
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