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- PDB-4na6: 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: 4na6 | ||||||
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Title | Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E749N | ||||||
![]() | Poly(ADP-ribose) glycohydrolase | ||||||
![]() | HYDROLASE / Poly(ADP-ribose) glycohydrolase / PARG | ||||||
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 / cytoplasm / cytosol 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 | ![]() | 410.9 KB | Display | ![]() |
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PDB format | ![]() | 337.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fc2SC ![]() 4n9yC ![]() 4n9zC ![]() 4na0C ![]() 4na4C ![]() 4na5C S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60132.574 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: E749N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O88622, poly(ADP-ribose) glycohydrolase #2: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M (NH4)2SO4, 16% PEG 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 43004 / Num. obs: 40639 / % possible obs: 94.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible all: 59.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4FC2 Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.227 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 104.17 Å2 / Biso mean: 36.8776 Å2 / Biso min: 11.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.484→2.549 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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