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Yorodumi- PDB-3uel: Crystal structure of the catalytic domain of rat poly (ADP-ribose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uel | ||||||
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Title | Crystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase bound to ADP-HPD | ||||||
Components | Poly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE / mammalian PARG / macrodomain / ADP-HPD | ||||||
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: 3 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 | 3uel.cif.gz | 620.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uel.ent.gz | 514.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uel_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3uel_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3uel_validation.xml.gz | 57 KB | Display | |
Data in CIF | 3uel_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3uel ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3uel | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 67780.156 Da / Num. of mol.: 3 / 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 #2: Chemical | |
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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: 2.58 Å3/Da / Density % sol: 52.24 % |
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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. 200 uM ADP-HPD, 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: 3→30 Å / Num. obs: 35972 / % possible obs: 90.1 % |
Reflection shell | Resolution: 3→3.08 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 60.053 / SU ML: 0.474 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / 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: 106.691 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.081 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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