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Yorodumi- PDB-4j5q: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1, apo structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j5q | ||||||
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Title | TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1, apo structure | ||||||
Components | O-acetyl-ADP-ribose deacetylase 1 | ||||||
Keywords | HYDROLASE / DNA repair / cellular signalling / macro domain / glycohydrolase / poly-ADP ribose / PARP / ADP-ribose | ||||||
Function / homology | Function and homology information ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / DNA damage response ...ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / DNA damage response / nucleolus / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Schellenberg, M.J. / Appel, C.D. / Krahn, J. / Williams, R.S. | ||||||
Citation | Journal: Embo J. / Year: 2013 Title: Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease. Authors: Sharifi, R. / Morra, R. / Appel, C.D. / Tallis, M. / Chioza, B. / Jankevicius, G. / Simpson, M.A. / Matic, I. / Ozkan, E. / Golia, B. / Schellenberg, M.J. / Weston, R. / Williams, J.G. / ...Authors: Sharifi, R. / Morra, R. / Appel, C.D. / Tallis, M. / Chioza, B. / Jankevicius, G. / Simpson, M.A. / Matic, I. / Ozkan, E. / Golia, B. / Schellenberg, M.J. / Weston, R. / Williams, J.G. / Rossi, M.N. / Galehdari, H. / Krahn, J. / Wan, A. / Trembath, R.C. / Crosby, A.H. / Ahel, D. / Hay, R. / Ladurner, A.G. / Timinszky, G. / Williams, R.S. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j5q.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j5q.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4j5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j5q_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 4j5q_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 4j5q_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4j5q_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/4j5q ftp://data.pdbj.org/pub/pdb/validation_reports/j5/4j5q | HTTPS FTP |
-Related structure data
Related structure data | 4j5rC 4j5sC 2jyc 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16446.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf130, OARD1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Y530, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: 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: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.6 Details: 100mM sodium citrate, 20% isopropanol, 20% PEG 4000 , pH 5.6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.35→50 Å / Num. all: 35292 / Num. obs: 34621 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2JYC 2jyc Resolution: 1.35→30.055 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.1 / σ(F): 1.38 / Phase error: 18.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6861 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30.055 Å
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Refine LS restraints |
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LS refinement shell |
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