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- PDB-7ooz: Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ooz | ||||||||||||
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Title | Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzyloxo-2-chloropurine | ||||||||||||
![]() | Purine nucleoside phosphorylase DeoD-type | ||||||||||||
![]() | TRANSFERASE / inhibitor / complex | ||||||||||||
Function / homology | ![]() uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Narczyk, M. / Stefanic, Z. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium. Authors: Narczyk, M. / Wojtys, M.I. / Lescic Asler, I. / Zinic, B. / Luic, M. / Jagusztyn-Krynicka, E.K. / Stefanic, Z. / Bzowska, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.9 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 861.7 KB | Display | ![]() |
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Full document | ![]() | 867.1 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ooyC ![]() 7op9C ![]() 7opaC ![]() 6f4xS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25818.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700392 / 26695 / Gene: deoD, HP_1178 / Production host: ![]() ![]() References: UniProt: P56463, purine-nucleoside phosphorylase |
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-Non-polymers , 6 types, 319 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/05Q.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/05Q.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-05Q / | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 12% PEG 8000, 0,1 M Tris pH 7.6, 0.02M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→46.433 Å / Num. obs: 104465 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.132 / Χ2: 1.088 / Net I/σ(I): 8.67 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6f4x Resolution: 1.7→40.21 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.35 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.61 Å2 / Biso mean: 23.146 Å2 / Biso min: 9.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→40.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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