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Yorodumi- PDB-6f1k: Structure of ARTD2/PARP2 WGR domain bound to double strand DNA wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f1k | ||||||||||||
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Title | Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / ADP-ribosylation / DNA repair / DNA end joining / ARTD2 / non-phosphorylated DNA | ||||||||||||
Function / homology | Function and homology information hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) ...hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) / poly-ADP-D-ribose modification-dependent protein binding / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / decidualization / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Obaji, E. / Haikarainen, T. / Lehtio, L. | ||||||||||||
Funding support | Finland, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural basis for DNA break recognition by ARTD2/PARP2. Authors: Obaji, E. / Haikarainen, T. / Lehtio, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f1k.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1k.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1k ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 | x 6
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Unit cell |
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-Components
#1: Protein | Mass: 15056.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase |
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#2: DNA chain | Mass: 6134.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CL / |
#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: 3.56 Å3/Da / Density % sol: 65.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9 / Details: PEG MME 5000 0.1 M Na-acetate ethylene glyco |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 16127 / % possible obs: 99.9 % / Observed criterion σ(I): 1.46 / Redundancy: 9.71 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.085 / Net I/σ(I): 19.19 |
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 10 % / Rmerge(I) obs: 1.557 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.69 / Rrim(I) all: 1.55 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARP2 homology model Resolution: 2.2→19.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.092 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.313 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→19.98 Å
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