+Open data
-Basic information
Entry | Database: PDB / ID: 6oa0 | ||||||
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Title | Structure of human PARG complexed with JA2-9 | ||||||
Components | Poly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stegeman, R.A. / Jones, D.E. / Ellenberger, T. / Kim, I.K. / Tainer, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death. Authors: Houl, J.H. / Ye, Z. / Brosey, C.A. / Balapiti-Modarage, L.P.F. / Namjoshi, S. / Bacolla, A. / Laverty, D. / Walker, B.L. / Pourfarjam, Y. / Warden, L.S. / Babu Chinnam, N. / Moiani, D. / ...Authors: Houl, J.H. / Ye, Z. / Brosey, C.A. / Balapiti-Modarage, L.P.F. / Namjoshi, S. / Bacolla, A. / Laverty, D. / Walker, B.L. / Pourfarjam, Y. / Warden, L.S. / Babu Chinnam, N. / Moiani, D. / Stegeman, R.A. / Chen, M.K. / Hung, M.C. / Nagel, Z.D. / Ellenberger, T. / Kim, I.K. / 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 | 6oa0.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oa0.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 6oa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/6oa0 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oa0 | HTTPS FTP |
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-Related structure data
Related structure data | 6o9xC 6o9yC 6oa1C 6oa3C 6oakC 6oalC C: citing same article (ref.) |
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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: 61223.633 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 (E. coli) References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase |
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#2: Chemical | ChemComp-M1D / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.05 M PCTP pH 7.5, 0.1 M NaCl, 0.15 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 32976 / % possible obs: 99.1 % / Redundancy: 4 % / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.051 Å / Num. unique obs: 2218 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.956 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.16 / 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: 29.344 Å2
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Refinement step | Cycle: 1 / Resolution: 2→29.94 Å
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Refine LS restraints |
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