+Open data
-Basic information
Entry | Database: PDB / ID: 7kg0 | ||||||
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Title | Structure of human PARG complexed with PARG-131 | ||||||
Components | Poly(ADP-ribose) glycohydrolasePoly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information 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 / nuclear body / carbohydrate metabolic process / 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 / nuclear body / carbohydrate metabolic process / mitochondrial matrix / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Arvai, A. / Bommagani, S. / Brosey, C.A. / Jones, D.E. / Warden, L.S. / Ahmed, Z. / Tainer, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Prog.Biophys.Mol.Biol. / Year: 2021 Title: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Authors: Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kg0.cif.gz | 268 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kg0.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/7kg0 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/7kg0 | HTTPS FTP |
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-Related structure data
Related structure data | 7kfpC 7kg1C 7kg3C 7kg6C 7kg7C 7kg8C 7kxbC 7lg7C 4b1gS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 61020.375 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase | ||||
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#2: Chemical | ChemComp-WDA / | ||||
#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2020 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→39.92 Å / Num. obs: 59073 / % possible obs: 94.29 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.81 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.09772 / Rpim(I) all: 0.05325 / Rrim(I) all: 0.1119 / Net I/σ(I): 7.85 |
Reflection shell | Resolution: 1.66→1.719 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.141 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 4954 / CC1/2: 0.59 / CC star: 0.861 / Rpim(I) all: 0.6203 / Rrim(I) all: 1.306 / % possible all: 79.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B1G Resolution: 1.66→37.33 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.67 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→37.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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