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Yorodumi- PDB-3se2: Human poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3se2 | ||||||
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Title | Human poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with 6(5H)-phenanthridinone | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE / DIPHTHERIA TOXIN LIKE FOLD / NAD+ / ADP-RIBOSYLATION / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / innate immune response / negative regulation of gene expression / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. ...Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Siponen, M.I. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors. Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. ...Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3se2.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3se2.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 3se2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3se2 ftp://data.pdbj.org/pub/pdb/validation_reports/se/3se2 | HTTPS FTP |
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-Related structure data
Related structure data | 3goySC 3mhjC 3mhkC 3p0nC 3p0pC 3p0qC 3smiC 3smjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 1532 - 1720 / Label seq-ID: 5 - 193
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 22118.590 Da / Num. of mol.: 4 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 6 types, 164 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 0.2M KSCN, 0.1M Bis-Tris-Propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2009 / Details: mirrors and double crystal monochromator |
Radiation | Monochromator: Si-111 (double crystal) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. all: 40412 / Num. obs: 40412 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.111 / Rsym value: 0.166 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.416 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GOY Resolution: 2.3→34.57 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.918 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.994 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→34.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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