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Yorodumi- PDB-5mx8: Crystal structure of H. pylori purine nucleoside phosphorylase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mx8 | ||||||
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Title | Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-3 | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase / clinical isolate / Helicobacter pylori / dead-end-complex | ||||||
Function / homology | Function and homology information uridine phosphorylase / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Stefanic, Z. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: Int. J. Biol. Macromol. / Year: 2017 Title: Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori. Authors: Stefanic, Z. / Mikleusevic, G. / Luic, M. / Bzowska, A. / Lescic Asler, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mx8.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mx8.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 5mx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mx8_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 5mx8_full_validation.pdf.gz | 475.8 KB | Display | |
Data in XML | 5mx8_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5mx8_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mx8 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mx8 | HTTPS FTP |
-Related structure data
Related structure data | 5mx4SC 5mx6C S: Starting model for refinement C: citing same article (ref.) |
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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: 25817.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori (bacteria) References: UniProt: K2JXG0, UniProt: P56463*PLUS, purine-nucleoside phosphorylase | ||
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#2: Chemical | ChemComp-HPA / | ||
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | ChemComp-PG4 / #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: 4.78 Å3/Da / Density % sol: 74.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.2M NaCl, 0.1M Na/K phosphate pH 6.2, 50% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.541 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: May 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.311 Å / Num. obs: 20243 / % possible obs: 99.4 % / Redundancy: 14 % / Net I/σ(I): 15.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MX4 Resolution: 2.4→29.311 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.85 Å2 / Biso mean: 37.169 Å2 / Biso min: 19.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→29.311 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: 7
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