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- PDB-3e0q: Crystal structure of Schistosoma mansoni purine nucleoside phosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3e0q | ||||||
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Title | Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor | ||||||
![]() | Purine-nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / Monocyclic inhibitor / Glycosyltransferase | ||||||
Function / homology | ![]() guanosine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pereira, H.M. / Berdini, V. / Ferri, M.R. / Cleasby, A. / Garratt, R.C. | ||||||
![]() | ![]() Title: Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor. Authors: Pereira, H.M. / Berdini, V. / Ferri, M.R. / Cleasby, A. / Garratt, R.C. #1: ![]() Title: Structures for the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni causal agent of schistosomiasis. Authors: Pereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 143.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.1 KB | Display | ![]() |
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Full document | ![]() | 496.5 KB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 55.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tcvS 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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Unit cell |
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Components
#1: Protein | Mass: 31197.254 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9BMI9, purine-nucleoside phosphorylase #2: Chemical | ChemComp-DMS / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 18-20% PEG 1500, 20% Glycerol, 32mM Sodium acetate, pH 4.9-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2002 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→44.46 Å / Num. obs: 56943 / % possible obs: 94.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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 1TCV Resolution: 1.9→44.32 Å / Num. restraintsaints: 87047 / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.161 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.82 Å2 / Biso mean: 20.249 Å2 / Biso min: 5.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.32 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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