[English] 日本語
Yorodumi- PDB-5mx6: Crystal structure of H. pylori purine nucleoside phosphorylase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mx6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-2 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Stefanic, Z. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5mx6.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5mx6.ent.gz | 233.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mx6_validation.pdf.gz | 522.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5mx6_full_validation.pdf.gz | 538.3 KB | Display | |
Data in XML | 5mx6_validation.xml.gz | 56.4 KB | Display | |
Data in CIF | 5mx6_validation.cif.gz | 78.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mx6 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mx6 | HTTPS FTP |
-Related structure data
Related structure data | 5mx4SC 5mx8C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 25817.096 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori (bacteria) References: UniProt: K2JXG0, UniProt: P56463*PLUS, purine-nucleoside phosphorylase |
---|
-Non-polymers , 6 types, 537 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HPA / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.19 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.2M Li2SO4, 0.1M Na acetate pH 4.5, 50% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9781 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9781 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.41→34.805 Å / Num. obs: 67753 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.069 / Rrim(I) all: 0.156 / Net I/σ(I): 9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MX4 Resolution: 2.41→34.805 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.32
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.82 Å2 / Biso mean: 34.9271 Å2 / Biso min: 11.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.41→34.805 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
|