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Yorodumi- PDB-4b1i: Structure of human PARG catalytic domain in complex with OA-ADP-HPD -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b1i | ||||||
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Title | Structure of human PARG catalytic domain in complex with OA-ADP-HPD | ||||||
Components | POLY(ADP-RIBOSE) GLYCOHYDROLASEPoly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE / POLY ADP-RIBOSE | ||||||
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: 2.14 Å | ||||||
Authors | Brassington, C. / Ellston, J. / Hassall, G. / Holdgate, G. / Johnson, T. / McAlister, M. / 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 | 4b1i.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b1i.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 4b1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b1i ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b1i | HTTPS FTP |
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-Related structure data
Related structure data | 4a0dSC 4b1gC 4b1hC 4b1jC S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 494 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-A8P / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SIX MUTATIONS INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % / Description: NONE |
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Crystal grow | Details: 25% PEG 3350, 36.4MM PCTP-4, 63.6MM PCTP-10, 0.2M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 18, 2010 / Details: VARIMAXHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→94.29 Å / Num. obs: 31210 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.14→2.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / % possible all: 84.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A0D Resolution: 2.14→65.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.67 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 39.668 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→65.26 Å
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Refine LS restraints |
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