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Yorodumi- PDB-3blj: Crystal structure of human poly(ADP-ribose) polymerase 15, cataly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3blj | ||||||
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Title | Crystal structure of human poly(ADP-ribose) polymerase 15, catalytic fragment | ||||||
Components | Poly(ADP-ribose) polymerase 15 | ||||||
Keywords | TRANSFERASE / PARP / POLY(ADP-RIBOSE) POLYMERASE / BAL-3 / SGC / STRUCTURAL GENOMICS CONSORTIUM / Glycosyltransferase / NAD / Nucleus / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / 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.Biol.Chem. / Year: 2015 Title: Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein. Authors: Karlberg, T. / Klepsch, M. / Thorsell, A.G. / Andersson, C.D. / Linusson, A. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3blj.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3blj.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 3blj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3blj ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blj | HTTPS FTP |
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-Related structure data
Related structure data | 2pqfSC 2x5yC 3geyC 4x52C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25439.459 Da / Num. of mol.: 2 / Fragment: Catalytic domain: Residues 459-656 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N3, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 48.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Ammonium chloride, 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: MAX II / Beamline: I911-3 / Wavelength: 0.97908 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2007 / Details: Si mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 25446 / Num. obs: 25446 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.138 / Rsym value: 0.186 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5711 / Rsym value: 0.587 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PQF Resolution: 2.2→19.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.269 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.206 / 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: 24.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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