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- PDB-2oc4: Crystal structure of human purine nucleoside phosphorylase mutant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oc4 | |||||||||
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Title | Crystal structure of human purine nucleoside phosphorylase mutant H257D with Imm-H | |||||||||
![]() | Purine nucleoside phosphorylase | |||||||||
![]() | TRANSFERASE / purine nucleoside phosphorylase | |||||||||
Function / homology | ![]() nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / response to xenobiotic stimulus / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rinaldo-Matthis, A. / Almo, S.C. / Schramm, V.L. | |||||||||
![]() | ![]() Title: Neighboring Group Participation in the Transition State of Human Purine Nucleoside Phosphorylase Authors: Murkin, A.S. / Birck, M.R. / Rinaldo-Matthis, A. / Shi, W. / Taylor, E.A. / Almo, S.C. / Schramm, V.L. | |||||||||
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 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.6 KB | Display | ![]() |
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Full document | ![]() | 815.4 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a0wC ![]() 2a0xC ![]() 2a0yC ![]() 2oc9C ![]() 2on6C ![]() 1rr6S C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32161.818 Da / Num. of mol.: 1 / Fragment: purine nucleoside phosphorylase / Mutation: H257D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00491, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-IMH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.592→30 Å / Num. all: 20698 / Num. obs: 20554 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.071 / Χ2: 0.675 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.592→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1945 / Rsym value: 0.62 / Χ2: 0.383 / % possible all: 94.6 |
-Phasing
Phasing MR | Rfactor: 0.378 / Cor.coef. Fo:Fc: 0.749
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RR6 Resolution: 2.592→29.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.945 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2.592→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.592→2.659 Å / Total num. of bins used: 20
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