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Yorodumi- PDB-1a69: PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a69 | ||||||
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Title | PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE) | ||||||
Components | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
Keywords | GLYCOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / TRANSFERASE | ||||||
Function / homology | Function and homology information purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / DNA damage response / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (Sulphate) at 2.1 A resolution. Authors: Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a69.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a69.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a69_validation.pdf.gz | 563.5 KB | Display | wwPDB validaton report |
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Full document | 1a69_full_validation.pdf.gz | 594.3 KB | Display | |
Data in XML | 1a69_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1a69_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a69 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a69 | HTTPS FTP |
-Related structure data
Related structure data | 1ecpS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25850.748 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P0ABP8, 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: 3.67 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 Details: 28-35% AMMONIUM SULPHATE, 50 MM CITRATE BUFFER, PH 5.2-5.4, pH 5.3 PH range: 5.2-5.4 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion, hanging drop / Details: Cook, W.J., (1985) J. Biol. Chem., 260, 12968. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 281 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 668538 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.137 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.2 Å / Rsym value: 0.297 / % possible all: 98 |
Reflection | *PLUS Num. obs: 72585 / Num. measured all: 668538 / Rmerge(I) obs: 0.137 |
Reflection shell | *PLUS Rmerge(I) obs: 0.297 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ECP Resolution: 2.1→20 Å / Isotropic thermal model: 1 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 207 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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