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- PDB-4dkb: Crystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dkb | ||||||
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Title | Crystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+ | ||||||
![]() | Deoxyuridine triphosphatase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() | 65.6 KB | Display | ![]() |
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PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.6 KB | Display | ![]() |
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Full document | ![]() | 723.7 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dk2C ![]() 4dk4SC ![]() 4dl8C ![]() 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
#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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#2: Chemical | #3: Chemical | ChemComp-DUN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% w/v PEG3350, 0.2 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.831→48.416 Å / Num. all: 26775 / Num. obs: 26775 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 18.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DK4 Resolution: 1.831→48.416 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.031 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / 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: 200 Å2 / Biso mean: 21.4041 Å2 / Biso min: 5.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.831→48.416 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.831→1.879 Å / Total num. of bins used: 20
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