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Yorodumi- PDB-3c4h: Human poly(ADP-ribose) polymerase 3, catalytic fragment in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4h | ||||||
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Title | Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor DR2313 | ||||||
Components | Poly(ADP-ribose) polymerase 3 | ||||||
Keywords | TRANSFERASE / enzyme-inhibitor complex / catalytic fragment / Structural Genomics / Structural Genomics Consortium / SGC / Glycosyltransferase / NAD / Nucleus | ||||||
Function / homology | Function and homology information negative regulation of isotype switching / negative regulation of telomerase RNA reverse transcriptase activity / NAD+- protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation ...negative regulation of isotype switching / negative regulation of telomerase RNA reverse transcriptase activity / NAD+- protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / intercellular bridge / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic activity / regulation of mitotic spindle organization / telomere maintenance / centriole / nucleotidyltransferase activity / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Welin, M. / Weigelt, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3. Authors: Lehtio, L. / Jemth, A.S. / Collins, R. / Loseva, O. / Johansson, A. / Markova, N. / Hammarstrom, M. / Flores, A. / Holmberg-Schiavone, L. / Weigelt, J. / Helleday, T. / Schuler, H. / Karlberg, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c4h.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4h.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4h ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4h | HTTPS FTP |
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-Related structure data
Related structure data | 3c49C 3ce0C 3fhbC 2pa9 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: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic fragment: Residues 178-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3, ADPRT3, ADPRTL3 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase |
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#2: Chemical | ChemComp-DRL / |
#3: Chemical | ChemComp-DMS / |
#4: 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: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 18978 / Num. obs: 18978 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.22 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.64 / Num. unique all: 2442 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PA9 2pa9 Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.747 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.209 / 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: 25.402 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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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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