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Yorodumi- PDB-7opa: Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7opa | ||||||||||||
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Title | Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzylthiopurine | ||||||||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||||||||
Keywords | TRANSFERASE / inhibitor / complex | ||||||||||||
Function / homology | Function and homology information 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 Å | ||||||||||||
Authors | Narczyk, M. / Stefanic, Z. | ||||||||||||
Funding support | Poland, Croatia, 3items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7opa.cif.gz | 553.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7opa.ent.gz | 459.5 KB | Display | PDB format |
PDBx/mmJSON format | 7opa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7opa_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7opa_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7opa_validation.xml.gz | 112.5 KB | Display | |
Data in CIF | 7opa_validation.cif.gz | 156.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/7opa ftp://data.pdbj.org/pub/pdb/validation_reports/op/7opa | HTTPS FTP |
-Related structure data
Related structure data | 7ooyC 7oozC 7op9C 6f4xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 25818.105 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: deoD, HP_1178 / Production host: Escherichia coli (E. coli) References: UniProt: P56463, purine-nucleoside phosphorylase |
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-Non-polymers , 5 types, 1083 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 12% PEG 8000, Tris-HCl pH 7,0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 1, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→49.62 Å / Num. obs: 204075 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.189 / Χ2: 0.727 / Net I/σ(I): 9.79 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F4X Resolution: 2→49.62 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.46 / 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: 116.15 Å2 / Biso mean: 44.8743 Å2 / Biso min: 15.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→49.62 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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