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- PDB-4fc2: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fc2 | ||||||
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Title | Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain | ||||||
![]() | Poly(ADP-ribose) glycohydrolase | ||||||
![]() | HYDROLASE / mouse / PARG / poly(ADP-ribose) glycohydrolase | ||||||
Function / homology | ![]() 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Cheng, Z. / Xu, W. | ||||||
![]() | ![]() Title: Crystallographic and biochemical analysis of the mouse poly(ADP-ribose) glycohydrolase. Authors: Wang, Z. / Gagne, J.P. / Poirier, G.G. / Xu, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 871.8 KB | Display | ![]() |
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PDB format | ![]() | 749.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4n9yC ![]() 4n9zC ![]() 4na0C ![]() 4na4C ![]() 4na5C ![]() 4na6C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60512.582 Da / Num. of mol.: 4 / Fragment: unp residues 439-959 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O88622, poly(ADP-ribose) glycohydrolase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M (NH4)2SO4, 16% PEG3,350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2012 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 187938 / Num. obs: 173052 / % possible obs: 92.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 |
Reflection shell | Resolution: 1.91→1.98 Å / % possible all: 54.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.22 Å2 / Biso mean: 38.528 Å2 / Biso min: 15.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.913→1.963 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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