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Open data
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Basic information
Entry | Database: PDB / ID: 6hh6 | ||||||
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Title | Human poly(ADP-ribose) glycohydrolase in complex with ADP-HPM | ||||||
![]() | Poly(ADP-ribose) glycohydrolase | ||||||
![]() | HYDROLASE / ADP-ribosylation / ADP-ribose / PARG / ADP-HPM | ||||||
Function / homology | ![]() nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ariza, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Authors: Rack, J.G.M. / Ariza, A. / Drown, B.S. / Henfrey, C. / Bartlett, E. / Shirai, T. / Hergenrother, P.J. / Ahel, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.3 KB | Display | ![]() |
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PDB format | ![]() | 184.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.9 KB | Display | ![]() |
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Full document | ![]() | 747.6 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g1pC ![]() 6g1qC ![]() 6g28C ![]() 6g2aC ![]() 6hgzC ![]() 6hh3C ![]() 6hh4C ![]() 6hh5C ![]() 6hozC ![]() 5a7rS 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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Unit cell |
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Components
#1: Protein | Mass: 60944.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase | ||
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#2: Chemical | ChemComp-A3R / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→54.09 Å / Num. obs: 50546 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.064 / Rrim(I) all: 0.239 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.674 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3055 / CC1/2: 0.597 / Rpim(I) all: 1.15 / Rrim(I) all: 2.916 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A7R Resolution: 1.85→54.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.491 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / 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: 24.94 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→54.15 Å
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Refine LS restraints |
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