+Open data
-Basic information
Entry | Database: PDB / ID: 4a0d | ||||||
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Title | Structure of unliganded human PARG catalytic domain | ||||||
Components | POLY(ADP-RIBOSE) GLYCOHYDROLASEPoly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE | ||||||
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: 1.75 Å | ||||||
Authors | Brassington, C. / Ellston, J. / Hassall, G. / Holdgate, G. / McAlister, M. / Overman, R. / Smith, G. / Tucker, J.A. / Watson, M. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structures of the Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by Adp-Hpd Derivatives. Authors: Tucker, J.A. / Bennett, N. / Brassington, C. / Durant, S.T. / Hassall, G. / Holdgate, G. / Mcalister, M. / Nissink, J.W.M. / Truman, C. / Watson, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a0d.cif.gz | 223.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a0d.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0d ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0d | HTTPS FTP |
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-Related 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: 60944.258 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 448-976 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-6HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase | ||||||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 616 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 617 TO ALA ...ENGINEERED | Sequence details | SIX MUTATIONS INTRODUCED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.54 % Description: STRUCTURE SOLVED BY MOLECULAR REPLACEMENT USING COORDINATES FROM SEMET MAD DETERMINATION IN ALTERNATIVE SPACE GROUP |
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Crystal grow | Details: 25% PEG 3350, 36.4MM PCTP 4, 63.6MM PCTP 10, 0.2M MG(SO4)2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.89 Å / Num. obs: 57354 / % possible obs: 97.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.954 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.652 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→46.89 Å
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