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Yorodumi- PDB-4f0e: Human ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f0e | ||||||
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Title | Human ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN IN COMPLEX WITH STO1102 | ||||||
Components | Poly [ADP-ribose] polymerase 15 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ARTD / PARP / POLY (ADP-RIBOSE) POLYMERASE / ADP-RIBOSE / BAL3 / B-AGGRESSIVE LYMPHOMA PROTEIN 3 / TRANSFERASE / GLYCOSYLTRANSFERASE / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+ 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: 2.4 Å | ||||||
Authors | Karlberg, T. / Andersson, C.D. / Lindgren, A. / Thorsell, A.G. / Ekblad, T. / Spjut, S. / Weigelt, J. / Elofsson, M. / Linusson, A. / Schuler, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening. Authors: Andersson, C.D. / Karlberg, T. / Ekblad, T. / Lindgren, A.E. / Thorsell, A.G. / Spjut, S. / Uciechowska, U. / Niemiec, M.S. / Wittung-Stafshede, P. / Weigelt, J. / Elofsson, M. / Schuler, H. / Linusson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f0e.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f0e.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 4f0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/4f0e ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f0e | HTTPS FTP |
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-Related structure data
Related structure data | 4f1lC 4f1qC 3bljS 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: 22967.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAL3, PARP15 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE / References: UniProt: Q460N3, 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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 10.5 Details: 40% 2-methyl-1,3-propanediol, 0.1 M CAPS, 2mM STO1102, pH 10.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 / Details: mirrors |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93928 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 30110 / Num. obs: 30110 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1988 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BLJ Resolution: 2.4→38.028 Å / σ(F): 0 / σ(I): 0 / Phase error: 29.76 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.956 Å2 / ksol: 0.391 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→38.028 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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