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Yorodumi- PDB-3ooh: Crystal structure of E. Coli purine nucleoside phosphorylase with PO4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ooh | ||||||
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Title | Crystal structure of E. Coli purine nucleoside phosphorylase with PO4 | ||||||
Components | Purine nucleoside phosphorylase deoD-type | ||||||
Keywords | TRANSFERASE / Purine nucleoside phosphorylase / phosphorylase | ||||||
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 / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Mikleusevic, G. / Stefanic, Z. / Narzyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M. | ||||||
Citation | Journal: Biochimie / Year: 2011 Title: Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies. Authors: Mikleusevic, G. / Stefanic, Z. / Narczyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ooh.cif.gz | 800.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ooh.ent.gz | 664.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ooh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ooh_validation.pdf.gz | 556.8 KB | Display | wwPDB validaton report |
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Full document | 3ooh_full_validation.pdf.gz | 628.3 KB | Display | |
Data in XML | 3ooh_validation.xml.gz | 155.1 KB | Display | |
Data in CIF | 3ooh_validation.cif.gz | 209.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/3ooh ftp://data.pdbj.org/pub/pdb/validation_reports/oo/3ooh | HTTPS FTP |
-Related structure data
Related structure data | 3onvC 3ooeC 3opvC 1k9sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25721.633 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: deoD, EcDH1_3614 / Plasmid: pSE380 / Production host: Escherichia coli (E. coli) / Strain (production host): HS533 References: UniProt: C9QST6, UniProt: P0ABP8*PLUS, purine-nucleoside phosphorylase #2: Chemical | ChemComp-PO4 / #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: 2.3 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 55-75% ammonium phosphate, 50mM citric buffer, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.32 % / Number: 262054 / Rmerge(I) obs: 0.137 / D res high: 2.9 Å / D res low: 55.72 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→48.2 Å / Num. obs: 89913 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 39.2
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K9S Resolution: 2.9→48.163 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.875 / SU ML: 2.91 / σ(F): 1.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.332 Å2 / ksol: 0.326 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.1 Å2 / Biso mean: 21.752 Å2 / Biso min: 4.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→48.163 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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