+Open data
-Basic information
Entry | Database: PDB / ID: 4b1g | ||||||
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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 / MAD / Resolution: 1.83 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 | 4b1g.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b1g.ent.gz | 182.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b1g ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b1g | 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: 61460.094 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 B (bacteria) / Strain (production host): B834(DE3) References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase |
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#2: Chemical | ChemComp-DTV / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 616 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 617 TO ALA ...ENGINEERED |
Nonpolymer details | DTV: DTT FROM PROTEIN BUFFER DERIVATISES CYSTEINE TO FORM (2R)-2-AZANIUMYL-3-[[(2S,3S)-2,3- ...DTV: DTT FROM PROTEIN BUFFER DERIVATISE |
Sequence details | SIX SURFACE ENTROPY MUTATIONS INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.81 % / Description: NONE |
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Crystal grow | Details: 28% PEG3350, 0.2M MAGNESIUM CHLORIDE, 0.1M PCTP (0.04M SODIUM PROPIONATE, 0.02M SODIUM CACODYLATE, 0.04M BIS-TRIS PROPANE) PH 7.5; 1:1 RATIO; 4 MICROLITRE DROP; ROOM TEMPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979, 0.975, 0.982 | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 19, 2009 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.83→88.99 Å / Num. obs: 39497 / % possible obs: 86.3 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4 | ||||||||||||
Reflection shell | Resolution: 1.83→1.93 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 47.9 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.83→66.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.77 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.14 / 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: 26.243 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→66.43 Å
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Refine LS restraints |
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