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Yorodumi- PDB-6g7x: Crystal structure of H. pylori purine nucleoside phosphorylase so... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g7x | ||||||
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Title | Crystal structure of H. pylori purine nucleoside phosphorylase soaked in PO4 | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / Purine nucleoside phosphorylase / H. pylori | ||||||
Function / homology | Function and homology information uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å | ||||||
Authors | Stefanic, Z. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: Croatica Chemica Acta / Year: 2018 Title: The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori Authors: Bosnjakovic, M. / Lescic Asler, I. / Stefanic, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g7x.cif.gz | 298.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g7x.ent.gz | 242.1 KB | Display | PDB format |
PDBx/mmJSON format | 6g7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g7x ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g7x | HTTPS FTP |
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-Related structure data
Related structure data | 6f52S 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
#1: Protein | Mass: 25818.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Gene: deoD, HP_1178 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P56463, purine-nucleoside phosphorylase #2: Chemical | ChemComp-IMD / #3: Chemical | ChemComp-PO4 / #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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 mol L-1 imidazole, 40% (w/v) polypropylene glycol (PPG) 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→60.64 Å / Num. obs: 133830 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.348 / Num. unique obs: 19209 / CC1/2: 0.936 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F52 Resolution: 1.762→46.753 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.07 Å2 / Biso mean: 18.9557 Å2 / Biso min: 5.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.762→46.753 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: 14
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