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Yorodumi- PDB-4abk: HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITH ADENO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4abk | ||||||
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Title | HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITH ADENOSINE- 5-DIPHOSPHORIBOSE | ||||||
Components | POLY [ADP-RIBOSE] POLYMERASE 14 | ||||||
Keywords | TRANSFERASE / PARP14 / ARTD8 | ||||||
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+ 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+ 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Karlberg, T. / Moche, M. / Thorsell, A.G. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Weigelt, J. / Schuler, H. | ||||||
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.H. / 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 | 4abk.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4abk.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 4abk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/4abk ftp://data.pdbj.org/pub/pdb/validation_reports/ab/4abk | HTTPS FTP |
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-Related structure data
Related structure data | 3q6zC 3q71C 3v2bC 3vfqC 4ablC 4d86C 3kh6 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: 19808.555 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN 3, RESIDUES 1208-1388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase |
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#2: Chemical | ChemComp-AR6 / [( |
#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: 1.86 Å3/Da / Density % sol: 33.94 % / Description: NONE |
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Crystal grow | Details: 1.4M TRI-SODIUM CITRATE, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35 Å / Num. obs: 18999 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 9.6 / % possible all: 64.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KH6 3kh6 Resolution: 1.6→32.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.366 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / 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: 18.599 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→32.84 Å
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