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- PDB-3iex: Schistosoma Purine nucleoside phosphorylase in complex with guanosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 3iex | ||||||
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Title | Schistosoma Purine nucleoside phosphorylase in complex with guanosine | ||||||
![]() | Purine-nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / Purine nucleoside phosphorylase / Glycosyltransferase | ||||||
Function / homology | ![]() guanosine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Castilho, M.S. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D. | ||||||
![]() | ![]() Title: Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: kinetic and structural studies Authors: Castilho, M.S. / Postigo, M.P. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.7 KB | Display | ![]() |
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PDB format | ![]() | 280.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3djfC ![]() 1td1S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 3 molecules ABC
#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 |
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-Non-polymers , 5 types, 571 molecules ![](data/chem/img/GMP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% PEG 1500, 20% GLYCEROL, 32mM SODIUM ACETATE, pH 4.9-5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K PH range: 4.9-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 44386 / % possible obs: 94.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.049 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TD1 Resolution: 2.05→43.628 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.844 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.849 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135 Å2 / Biso mean: 37.868 Å2 / Biso min: 15.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→43.628 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: 16
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