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Yorodumi- PDB-7l9i: Crystal structure of human ARH3-D314A bound to magnesium and ADP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l9i | ||||||
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Title | Crystal structure of human ARH3-D314A bound to magnesium and ADP-ribose | ||||||
Components | ADP-ribose glycohydrolase ARH3 | ||||||
Keywords | HYDROLASE / ADP-ribose / calcium | ||||||
Function / homology | Function and homology information ADP-ribosylserine hydrolase activity / peptidyl-serine ADP-deribosylation / O-acetyl-ADP-ribose deacetylase activity / cellular response to superoxide / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage ...ADP-ribosylserine hydrolase activity / peptidyl-serine ADP-deribosylation / O-acetyl-ADP-ribose deacetylase activity / cellular response to superoxide / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / POLB-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / hydrolase activity, hydrolyzing O-glycosyl compounds / nuclear body / mitochondrial matrix / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pourfarjam, Y. / Kurinov, I. / Moss, J. / Kim, I.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 reveals the basis of metal selectivity and different roles for the two magnesium ions. Authors: Pourfarjam, Y. / Ma, Z. / Kurinov, I. / Moss, J. / Kim, I.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l9i.cif.gz | 601.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l9i.ent.gz | 398.1 KB | Display | PDB format |
PDBx/mmJSON format | 7l9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/7l9i ftp://data.pdbj.org/pub/pdb/validation_reports/l9/7l9i | HTTPS FTP |
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-Related structure data
Related structure data | 7l9fC 7l9hC 6d36S 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 39233.953 Da / Num. of mol.: 4 / Mutation: D314A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRS, ADPRHL2, ARH3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NX46, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, poly(ADP-ribose) glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | ChemComp-AR6 / [( #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate buffer pH 4.5, 0.1 M MgCl2, and 24 % polyethylene glycol (PEG) 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→67.64 Å / Num. obs: 112761 / % possible obs: 89.77 % / Redundancy: 1.9 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 11030 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D36 Resolution: 1.8→67.64 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.183 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→67.64 Å
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Refine LS restraints |
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LS refinement shell |
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