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Open data
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Basic information
Entry | Database: PDB / ID: 1vfn | ||||||
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Title | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
![]() | PURINE-NUCLEOSIDE PHOSPHORYLASE | ||||||
![]() | NUCLEOSIDE PHOSPHORYLASE / TRANSFERASE / GLYCOSYLTRANSFERASE / DISEASE MUTATION | ||||||
Function / homology | ![]() guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koellner, G. / Bzowska, A. | ||||||
![]() | ![]() Title: Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution. Authors: Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A. #1: ![]() Title: Calf Spleen Purine Nucleoside Phosphorylase: Purification, Sequence and Crystal Structure of its Complex with an N(7)-Acycloguanosine Inhibitor Authors: Bzowska, A. / Luic, M. / Schroder, W. / Shugar, D. / Saenger, W. / Koellner, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.4 KB | Display | ![]() |
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PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.6 KB | Display | ![]() |
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Full document | ![]() | 401.4 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ulbS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31312.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P55859, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-HPA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 16%(W/V) PEG 4000, 0.04M TRIS-HCL BUFFER PH 8.2-8.5, 0.08M MGCL2, pH 8.0 PH range: 8.2-8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9204 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 15158 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 3.27 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ULB Resolution: 2.15→20 Å / Isotropic thermal model: TNT PACKAGE / σ(F): 1 / Stereochemistry target values: TNT PACKAGE
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Solvent computation | Solvent model: TNT PACKAGE / Bsol: 173 Å2 / ksol: 0.665 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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