+Open data
-Basic information
Entry | Database: PDB / ID: 1b8o | |||||||||
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Title | PURINE NUCLEOSIDE PHOSPHORYLASE | |||||||||
Components | PURINE NUCLEOSIDE PHOSPHORYLASE | |||||||||
Keywords | TRANSFERASE / PENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE | |||||||||
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: 1.5 Å | |||||||||
Authors | Fedorov, A.A. / Kicska, G.A. / Fedorov, E.V. / Shi, W. / Tyler, P.C. / Furneaux, R.H. / Schramm, V.L. / Almo, S.C. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Authors: Fedorov, A. / Shi, W. / Kicska, G. / Fedorov, E. / Tyler, P.C. / Furneaux, R.H. / Hanson, J.C. / Gainsford, G.J. / Larese, J.Z. / Schramm, V.L. / Almo, S.C. #1: Journal: Biochemistry / Year: 1998 Title: Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues. Authors: Mao, C. / Cook, W.J. / Zhou, M. / Federov, A.A. / Almo, S.C. / Ealick, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8o.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8o.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8o_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 1b8o_full_validation.pdf.gz | 461.2 KB | Display | |
Data in XML | 1b8o_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1b8o_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8o ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8o | HTTPS FTP |
-Related structure data
Related structure data | 1pbnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31687.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEXED WITH TRANSITION-STATE ANALOGUE 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL Source: (natural) Bos taurus (cattle) / Organ: SPLEEN References: UniProt: P55859, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-IMH / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: PEG-400, TRIS, MGCL2, K3PO4, pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.04019 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04019 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 42526 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PBN Resolution: 1.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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