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- PDB-1yr3: Escherichia coli purine nucleoside phosphorylase II, the product ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yr3 | ||||||
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Title | Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene | ||||||
![]() | Xanthosine phosphorylase | ||||||
![]() | TRANSFERASE / purine nucleoside phosphorylase guanine xanthine | ||||||
Function / homology | ![]() 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 / protein hexamerization / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dandanell, G. / Szczepanowski, R.H. / Kierdaszuk, B. / Shugar, D. / Bochtler, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.7 KB | Display | ![]() |
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PDB format | ![]() | 251.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 509.1 KB | Display | ![]() |
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Full document | ![]() | 555.3 KB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 78.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yqqSC ![]() 1yquC S: Starting model for refinement C: citing same article ( |
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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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Details | a hexamer with 32 point symmetry that results from the dimerization of trimers |
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Components
#1: Protein | Mass: 29865.590 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P45563, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-XAN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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