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- PDB-1pke: Crystal Structure of E. coli purine nucleoside phosphorylase comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pke | ||||||
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Title | Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and sulfate/phosphate | ||||||
![]() | Purine nucleoside phosphorylase DeoD-type | ||||||
![]() | TRANSFERASE / hexamer / protein-nucleoside complex / trimer of dimers | ||||||
Function / homology | ![]() purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bennett, E.M. / Li, C. / Allan, P.W. / Parker, W.B. / Ealick, S.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.4 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pk7C ![]() 1pk9C ![]() 1pr0C ![]() 1pr1C ![]() 1pr2C ![]() 1pr4C ![]() 1pr5C ![]() 1pr6C ![]() 1pw7C ![]() 1ecpS 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 | The biological hexamer is generated from the asymmetric unit trimer by the operation: X,X-Y,1/6-Z |
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Components
#1: Protein | Mass: 25721.633 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P0ABP9, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.15 % | ||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
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: 2.3→6 Å / Num. all: 45873 / Num. obs: 36786 / % possible obs: 80.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique all: 1641 / % possible all: 36.2 |
Reflection | *PLUS Num. obs: 39577 / % possible obs: 84.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ECP Resolution: 2.3→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: 2.3→6 Å
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Refinement | *PLUS Rfactor Rwork: 0.191 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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