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Yorodumi- PDB-4rj2: Crystal structure of E.coli purine nucleoside phosphorylase at 0.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rj2 | ||||||
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Title | Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / phosphorylase | ||||||
Function / homology | Nucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | ||||||
Authors | Timofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution Authors: Timofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rj2.cif.gz | 575.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rj2.ent.gz | 478.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/4rj2 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/4rj2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25721.633 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoD / Production host: Escherichia coli (E. coli) References: UniProt: H0QGF5, purine-nucleoside phosphorylase #2: Chemical | ChemComp-GOL / #3: 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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Method: counter-diffusion / Details: COUNTER DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→20 Å / Num. obs: 718472 / % possible obs: 98.41 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 0.99→1.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.11 / Num. unique all: 104431 / % possible all: 98.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→16.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / 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: 11.135 Å2
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Refinement step | Cycle: LAST / Resolution: 0.99→16.28 Å
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