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Yorodumi- PDB-2qpl: Crystal structure of calf spleen purine nucleoside phosphorylase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qpl | ||||||
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Title | Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Purine Nucleoside Phosphorylase / Acetylation / Glycosyltransferase | ||||||
Function / homology | Function and homology information guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pereira, H.M. / Berdini, V. / Cleasby, A. / Garratt, R.C. | ||||||
Citation | Journal: Febs Lett. / Year: 2007 Title: Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue. Authors: Pereira, H.M. / Berdini, V. / Cleasby, A. / Garratt, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qpl.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qpl.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 2qpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qpl ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qpl | HTTPS FTP |
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-Related structure data
Related structure data | 1a9rS 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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Details | The biological assembly is a trimer generated from the monomer by the crystallographic operations |
-Components
#1: Protein | Mass: 31427.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P55859, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-BTY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA-D-GLUCOPYRANOSIDE , pH 8.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2002 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→66.074 Å / Num. obs: 15761 / % possible obs: 97.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a9r Resolution: 2.1→46.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.905 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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