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Open data
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Basic information
Entry | Database: PDB / ID: 1b8n | ||||||
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Title | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
![]() | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
![]() | TRANSFERASE / PENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
Function / homology | ![]() guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Kicska, G.A. / Fedorov, E.V. / Strokopytov, B.V. / Tyler, P.C. / Furneaux, R.H. / Schramm, V.L. / Almo, S.C. | ||||||
![]() | ![]() Title: Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase Authors: Kicska, G.A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Shi, W. / Fedorov, A.A. / Lewandowicz, A. / Cahill, S.M. / Almo, S.C. / Schramm, V.L. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.3 KB | Display | ![]() |
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Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pbnS 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
#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-DEAZAGUANIN-9-YL)-D-RIBITOL Source: (natural) ![]() ![]() References: UniProt: P55859, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-IMG / |
#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: pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Fedorov, R.H., (2001) Biochemistry, 40, 853. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 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: 2→20 Å / Num. obs: 16237 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 |
Reflection | *PLUS % possible obs: 86.8 % / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 76.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PBN Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.296 / % reflection Rfree: 5 % / Rfactor Rwork: 0.241 |