[English] 日本語
Yorodumi- PDB-1pw7: Crystal Structure of E. coli purine nucleoside phosphorylase comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pw7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 9-beta-D-arabinofuranosyladenine and sulfate/phosphate | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / protein-nucleoside complex | ||||||
Function / homology | Function and homology information purine nucleoside metabolic process / nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pw7.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pw7.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pw7 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pw7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1pk7C 1pk9C 1pkeC 1pr0C 1pr1C 1pr2C 1pr4C 1pr5C 1pr6C 1ecpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Details | The biological hexamer is generated from the asymmetric unit trimer by the operation: 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.84 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: ammonium sulfate, citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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→6 Å / Num. all: 68924 / Num. obs: 55951 / % possible obs: 81.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 56.3 |
Reflection | *PLUS Num. obs: 58708 / % possible obs: 82.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Mean I/σ(I) obs: 4.4 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ECP Resolution: 2→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: WARNING B-factors for the ligand RAB are high, especially in subunits A and B, suggesting significant variation in the position of these ligand atoms.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
| ||||||||||||||||||||
Refine LS restraints | *PLUS
|