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Yorodumi- PDB-1rfg: Crystal Structure of Human Purine Nucleoside Phosphorylase Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rfg | ||||||
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Title | Crystal Structure of Human Purine Nucleoside Phosphorylase Complexed with Guanosine | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / DRUG DESIGN / SYNCHROTRON / GUANOSINE | ||||||
Function / homology | Function and homology information 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 / purine-nucleoside phosphorylase activity / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Canduri, F. / Silva, R.G. / Dos Santos, D.M. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of human PNP complexed with ligands. Authors: Canduri, F. / Silva, R.G. / dos Santos, D.M. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. #1: Journal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2003 Title: Crystal Structural of Human Purine Nucleoside Phosphorylase at 2.3 Angstrom Resolution Authors: de Azevedo Jr., W.F. / Canduri, F. / dos Santos, D.M. / Silva, R.G. / de Oliveira, J.S. / de Carvalho, L.P. / Basso, L.A. / Mendes, M.A. / Palma, M.S. / Santos, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rfg.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rfg.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rfg_validation.pdf.gz | 776.2 KB | Display | wwPDB validaton report |
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Full document | 1rfg_full_validation.pdf.gz | 797.4 KB | Display | |
Data in XML | 1rfg_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 1rfg_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rfg ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rfg | HTTPS FTP |
-Related structure data
Related structure data | 1v41C 1v45C 1pwyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32053.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Plasmid: PET-23A+ / Production host: Escherichia coli (E. coli) References: UniProt: P00491, purine-nucleoside phosphorylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GMP / | #4: 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: 4.68 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: AMMONIUM SULFATE, pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.431 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.224 Å / Num. obs: 14265 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 2.9→3.01 Å / Rmerge(I) obs: 0.214 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PWY Resolution: 2.9→7 Å / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.17 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3337 Å / Luzzati d res low obs: 7 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→7 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.9 Å
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