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Yorodumi- PDB-3uek: Crystal structure of the catalytic domain of rat poly (ADP-ribose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uek | ||||||
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Title | Crystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase | ||||||
Components | Poly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE / mammalian PARG / macrodomain | ||||||
Function / homology | Function and homology information POLB-Dependent Long Patch Base Excision Repair / nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / regulation of DNA repair / detection of bacterium / positive regulation of DNA repair / carbohydrate metabolic process / DNA damage response ...POLB-Dependent Long Patch Base Excision Repair / nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / regulation of DNA repair / detection of bacterium / positive regulation of DNA repair / carbohydrate metabolic process / DNA damage response / chromatin binding / chromatin / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Kim, I.K. / Kiefer, J.R. / Stegemann, R.A. / Classen, S. / Tainer, J.A. / Ellenberger, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Authors: Kim, I.K. / Kiefer, J.R. / Ho, C.M. / Stegeman, R.A. / Classen, S. / Tainer, J.A. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uek.cif.gz | 227.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uek.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uek_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3uek_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 3uek_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3uek_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3uek ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3uek | HTTPS FTP |
-Related 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: 67780.156 Da / Num. of mol.: 1 / Fragment: UNP residues 385-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Parg / Production host: Escherichia coli (E. coli) References: UniProt: Q9QYM2, poly(ADP-ribose) glycohydrolase |
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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: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16-20% PEG2000 monomethylether, 0.1M Tris-HCl pH7.5, 0.1M NaCl, 0.2M potassium thiocyanate., VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12712 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2011 |
Radiation | Monochromator: Cryo-cooled Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12712 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 43903 / % possible obs: 98.1 % |
Reflection shell | Resolution: 1.95→2 Å / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.187 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / 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: 47.149 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 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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