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Yorodumi- PDB-5a7r: Human poly(ADP-ribose) glycohydrolase in complex with synthetic d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a7r | ||||||
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Title | Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose | ||||||
Components | POLY(ADP-RIBOSE) GLYCOHYDROLASEPoly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE / PARG / 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 / 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: 1.95 Å | ||||||
Authors | Lambrecht, M.J. / Brichacek, M. / Barkauskaite, E. / Ariza, A. / Ahel, I. / Hergenrother, P.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Synthesis of Dimeric Adp-Ribose and its Structure with Human Poly(Adp-Ribose) Glycohydrolase. Authors: Lambrecht, M.J. / Brichacek, M. / Barkauskaite, E. / Ariza, A. / Ahel, I. / Hergenrother, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a7r.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a7r.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a7r ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a7r | HTTPS FTP |
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-Related structure data
Related structure data | 4a0dS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60929.242 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase |
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-Non-polymers , 6 types, 449 molecules
#2: Chemical | #3: Chemical | ChemComp-BME / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PPI / #7: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 8 Details: 20% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2014 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SINGLE BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→55.22 Å / Num. obs: 44881 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A0D Resolution: 1.95→66.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.749 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WERE REFINED INDIVIDUALLY
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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: 22.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→66.19 Å
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Refine LS restraints |
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