+Open data
-Basic information
Entry | Database: PDB / ID: 8swy | ||||||
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Title | PARP4 ART domain bound to NADH | ||||||
Components | Protein mono-ADP-ribosyltransferase PARP4 | ||||||
Keywords | TRANSFERASE / PARP family / ADP-ribosyltransferase / marylation / vault | ||||||
Function / homology | Function and homology information regulation of telomerase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / protein modification process / spindle microtubule ...regulation of telomerase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / protein modification process / spindle microtubule / response to xenobiotic stimulus / inflammatory response / ribonucleoprotein complex / DNA repair / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Frigon, L. / Pascal, J.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP. Authors: Frigon, L. / Pascal, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8swy.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8swy.ent.gz | 250.1 KB | Display | PDB format |
PDBx/mmJSON format | 8swy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/8swy ftp://data.pdbj.org/pub/pdb/validation_reports/sw/8swy | HTTPS FTP |
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-Related structure data
Related structure data | 8swzC 8sx1C 8sx2C C: citing same article (ref.) |
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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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28647.484 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP4, ADPRTL1, KIAA0177, PARPL / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKK3, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | 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: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→46.41 Å / Num. obs: 58576 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.022 / Rrim(I) all: 0.067 / Χ2: 1.11 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.55→2.66 Å / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 1.426 / Num. measured all: 35054 / Num. unique obs: 3729 / CC1/2: 0.612 / Rpim(I) all: 0.486 / Rrim(I) all: 1.509 / Χ2: 0.83 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.41 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 30.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→46.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.9878 Å / Origin y: 12.5248 Å / Origin z: 29.213 Å
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Refinement TLS group | Selection details: all |