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Yorodumi- PDB-1yqu: Escherichia coli purine nucleoside phosphorylase II, the product ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yqu | ||||||
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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 catabolic process ...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 catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / protein hexamerization / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 | 1yqu.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yqu.ent.gz | 117 KB | Display | PDB format |
PDBx/mmJSON format | 1yqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/1yqu ftp://data.pdbj.org/pub/pdb/validation_reports/yq/1yqu | HTTPS FTP |
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-Related structure data
Related structure data | 1yqqC 1yr3C 4pnpS C: citing same article (ref.) S: Starting model for refinement |
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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.: 3 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 | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: Tris, PEG4K, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 4, 2002 |
Radiation | Monochromator: triangular monochromator, bent mirror (information from the Web-site) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→25 Å / Num. all: 15055 / Num. obs: 15055 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1436 / Rsym value: 0.382 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4PNP Resolution: 3.1→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→25 Å
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