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Yorodumi- PDB-1pr4: Escherichia coli Purine Nucleoside Phosphorylase Complexed with 9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pr4 | ||||||
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Title | Escherichia coli Purine Nucleoside Phosphorylase Complexed with 9-beta-D-ribofuranosyl-6-methylthiopurine and Phosphate/Sulfate | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / protein-nucleoside complex | ||||||
Function / homology | Function and homology information purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bennett, E.M. / Li, C. / Allan, P.W. / Parker, W.B. / Ealick, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. Authors: Bennett, E.M. / Li, C. / Allan, P.W. / Parker, W.B. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pr4.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pr4.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pr4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1pr4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1pr4_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 1pr4_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/1pr4 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/1pr4 | HTTPS FTP |
-Related structure data
Related structure data | 1pk7C 1pk9C 1pkeC 1pr0C 1pr1C 1pr2C 1pr5C 1pr6C 1pw7C 1ecpS 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 on special symmetry positions |
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Details | The biological hexamer is generated from the trimer in the PDB file by the following operator: x,x-y,1/6-z |
-Components
#1: Protein | Mass: 25981.947 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli O157:H7 (bacteria) / Genus: Escherichia, Escherichia / Species: , Escherichia coli References: UniProt: P0ABP9, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.26 Å3/Da / Density % sol: 62.26 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: citrate, ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 1996 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→6 Å / Num. all: 38546 / Num. obs: 35778 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.48 Å / % possible all: 94 |
Reflection | *PLUS Num. obs: 40906 / % possible obs: 94 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Mean I/σ(I) obs: 13.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ECP Resolution: 2.4→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refinement | *PLUS Rfactor Rwork: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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