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Yorodumi- PDB-1yr3: Escherichia coli purine nucleoside phosphorylase II, the product ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yr3 | ||||||
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Title | Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene | ||||||
Components | Xanthosine phosphorylase | ||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase guanine xanthine | ||||||
Function / homology | Function and homology information guanosine catabolic process / xanthosine catabolic process / inosine nucleosidase activity / deoxyguanosine catabolic process / deoxyinosine catabolic process / inosine catabolic process / nucleobase-containing small molecule metabolic process / guanosine phosphorylase activity / nucleobase-containing small molecule interconversion / purine-nucleoside phosphorylase ...guanosine catabolic process / xanthosine catabolic process / inosine nucleosidase activity / deoxyguanosine catabolic process / deoxyinosine catabolic process / inosine catabolic process / nucleobase-containing small molecule metabolic process / guanosine phosphorylase activity / nucleobase-containing small molecule interconversion / purine-nucleoside phosphorylase / purine nucleoside catabolic process / protein hexamerization / purine-nucleoside phosphorylase activity / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Dandanell, G. / Szczepanowski, R.H. / Kierdaszuk, B. / Shugar, D. / Bochtler, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene Authors: Dandanell, G. / Szczepanowski, R.H. / Kierdaszuk, B. / Shugar, D. / Bochtler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yr3.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yr3.ent.gz | 251.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/1yr3 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/1yr3 | HTTPS FTP |
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-Related structure data
Related structure data | 1yqqSC 1yquC 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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Details | a hexamer with 32 point symmetry that results from the dimerization of trimers |
-Components
#1: Protein | Mass: 29865.590 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xapA, pndA / Plasmid: PGD265 / Production host: Escherichia coli (E. coli) / Strain (production host): GD1524 References: UniProt: P45563, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-XAN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: TRIS, Li2SO4, PEG4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 11, 2002 / Details: Osmic MaxFlux |
Radiation | Monochromator: Osmic Max Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 35998 / Num. obs: 35998 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 123.4 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1750 / Rsym value: 0.357 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YQQ Resolution: 3.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→25 Å
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