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Yorodumi- PDB-3iny: Crystal structure of human purine nucleoside phosphorylase in com... -
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-Basic information
Entry | Database: PDB / ID: 3iny | ||||||
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Title | Crystal structure of human purine nucleoside phosphorylase in complex with 7-deazaguanine | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / 7-deazaguanine / Cytoskeleton / Disease mutation / Glycosyltransferase | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | de Azevedo Jr, W.F. / Santos, D.S. / Basso, L.A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Crystal structure and molecular dynamics studies of human purine nucleoside phosphorylase complexed with 7-deazaguanine. Authors: Caceres, R.A. / Timmers, L.F. / Pauli, I. / Gava, L.M. / Ducati, R.G. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iny.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iny.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iny_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 3iny_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 3iny_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3iny_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3iny ftp://data.pdbj.org/pub/pdb/validation_reports/in/3iny | HTTPS FTP |
-Related structure data
Related structure data | 1v41S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32184.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Production host: Escherichia coli (E. coli) References: UniProt: P00491, purine-nucleoside phosphorylase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-7DG / | #4: Water | ChemComp-HOH / | Sequence details | AUTHOR'S COORDINATES SEQUENCE HAS ONE CONFLICT G51S WITH DATABASE SEQUENCE P00491. AUTHOR DOES NOT ...AUTHOR'S COORDINATE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.59 Å3/Da / Density % sol: 73.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Hanging drops were prepared mixing 1 microL of protein solution and 1 microL of reservoir solution containing 19% ammonium sulfate and 0.5 M sodium citrate pH 5.6. , VAPOR DIFFUSION, HANGING ...Details: Hanging drops were prepared mixing 1 microL of protein solution and 1 microL of reservoir solution containing 19% ammonium sulfate and 0.5 M sodium citrate pH 5.6. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2008 |
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: 2.75→47.95 Å / Num. all: 14793 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 11 |
Reflection shell | Highest resolution: 2.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 3.91 / Num. unique all: 15340 / Rsym value: 0.081 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V41 Resolution: 2.75→43.69 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.736 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.385 / ESU R Free: 0.301 / 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: 43.404 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→43.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20
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