+Open data
-Basic information
Entry | Database: PDB / ID: 1vfn | ||||||
---|---|---|---|---|---|---|---|
Title | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
Components | PURINE-NUCLEOSIDE PHOSPHORYLASEPurine nucleoside phosphorylase | ||||||
Keywords | NUCLEOSIDE PHOSPHORYLASE / TRANSFERASE / GLYCOSYLTRANSFERASE / DISEASE MUTATION | ||||||
Function / homology | Function and homology information guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Koellner, G. / Bzowska, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 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: Journal: FEBS Lett. / Year: 1995 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1vfn.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1vfn.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfn ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfn | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ulbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 31312.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: SPLEEN References: UniProt: P55859, purine-nucleoside phosphorylase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-HPA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9204 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ULB Resolution: 2.15→20 Å / Isotropic thermal model: TNT PACKAGE / σ(F): 1 / Stereochemistry target values: TNT PACKAGE
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: TNT PACKAGE / Bsol: 173 Å2 / ksol: 0.665 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|