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Yorodumi- PDB-1pk9: Crystal Structure of E. coli purine nucleoside phosphorylase comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pk9 | ||||||
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Title | Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoroadenosine and sulfate/phosphate | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / hexamer / protein-nucleoside complex / trimer of dimers | ||||||
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: 1.9 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 | 1pk9.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pk9.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/1pk9 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/1pk9 | HTTPS FTP |
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-Related structure data
Related structure data | 1pk7C 1pkeC 1pr0C 1pr1C 1pr2C 1pr4C 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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Details | The biological hexamer is generated from the asymmetric unit trimer by the operation: X,X-Y,1/6-Z |
-Components
#1: Protein | Mass: 25721.633 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: 3.37 Å3/Da / Density % sol: 63.46 % | ||||||||||||||||||||||||
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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
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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: 1.9→6 Å / Num. all: 81159 / Num. obs: 67754 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 57.8 |
Reflection | *PLUS Num. obs: 70788 / % possible obs: 85.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ECP Resolution: 1.9→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: 1.9→6 Å
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Refinement | *PLUS Rfactor Rfree: 0.264 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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