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Yorodumi- PDB-3q6z: HUman PARP14 (ARTD8)-Macro domain 1 in complex with adenosine-5-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q6z | ||||||
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Title | HUman PARP14 (ARTD8)-Macro domain 1 in complex with adenosine-5-diphosphoribose | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE / Structural Genomics Consortium / SGC / Adp-ribose binding | ||||||
Function / homology | Function and homology information positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / negative regulation of type II interferon-mediated signaling pathway / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / 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 / negative regulation of type II interferon-mediated signaling pathway / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / 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 / 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: 2.23 Å | ||||||
Authors | Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sehic, A. / Thorsell, A.G. / Tresaugues, L. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2013 Title: Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains. Authors: Forst, A.H. / Karlberg, T. / Herzog, N. / Thorsell, A.G. / Gross, A. / Feijs, K.L. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q6z.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q6z.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 3q6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q6z_validation.pdf.gz | 772.4 KB | Display | wwPDB validaton report |
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Full document | 3q6z_full_validation.pdf.gz | 773.4 KB | Display | |
Data in XML | 3q6z_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 3q6z_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q6z ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q6z | HTTPS FTP |
-Related structure data
Related structure data | 3q71C 3v2bC 3vfqC 4abkC 4ablC 4d86C 1spvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23514.178 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN 1, residues 708-898 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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#2: Chemical | ChemComp-APR / |
#3: 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: 1.93 Å3/Da / Density % sol: 36.39 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 30% PEGMME2000, 0.1M HEPES, 4mM ADP-RIBOSE, 4mM MAGNESIUM CHLORIDE, pH 8.5, 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 |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 28, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR, 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: 2.23→35 Å / Num. obs: 9427 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.079 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 12 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 5.5 / Num. unique all: 667 / Rsym value: 0.325 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SPV Resolution: 2.23→31.92 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.2 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→31.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.29 Å / Total num. of bins used: 20
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