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Yorodumi- PDB-3smi: Human poly(ADP-ribose) polymerase 14 (Parp14/Artd8) - catalytic d... -
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-Basic information
Entry | Database: PDB / ID: 3smi | ||||||
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Title | Human poly(ADP-ribose) polymerase 14 (Parp14/Artd8) - catalytic domain in complex with a quinazoline inhibitor | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / DIPHTHERIA TOXIN LIKE FOLD / TRANSFERASE / NAD+ / ADP-RIBOSYLATION / TRANSFERASE-TRANSFERASE Inhibitor complex / 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity ...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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Nordlund, P. ...Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Graslund, S. / Kouznetsova, E. / Nordlund, P. / Nyman, T. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / 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 | 3smi.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3smi.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3smi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3smi_validation.pdf.gz | 929.1 KB | Display | wwPDB validaton report |
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Full document | 3smi_full_validation.pdf.gz | 933.4 KB | Display | |
Data in XML | 3smi_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3smi_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/3smi ftp://data.pdbj.org/pub/pdb/validation_reports/sm/3smi | HTTPS FTP |
-Related structure data
Related structure data | 3goySC 3mhjC 3mhkC 3p0nC 3p0pC 3p0qC 3se2C 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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-Components
#1: Protein | Mass: 22118.590 Da / Num. of mol.: 2 / 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 #2: Chemical | #3: 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: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG3350, 0.2M NaNO3, 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: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 21, 2010 / Details: mirrors and double crystal monochromator |
Radiation | Monochromator: double crystals Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35 Å / Num. all: 16003 / Num. obs: 16003 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 39.21 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.179 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1155 / Rsym value: 0.462 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GOY Resolution: 2.4→33.67 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.362 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→33.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.57 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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