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Yorodumi- PDB-7aks: Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex wit... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 7aks | |||||||||
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| Title | Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide | |||||||||
Components |
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Keywords | HYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADPRHL2 / ADP-RIBOSYLHYDROLASE LIKE 2 / SER-ADPR / SERINE-ADPR / ADP-RIBOSYL-L-SERINE | |||||||||
| Function / homology | Function and homology informationcellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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 ...cellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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 / hydrolase activity, hydrolyzing O-glycosyl compounds / base-excision repair, gap-filling / 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: 1.86 Å | |||||||||
Authors | Ariza, A. | |||||||||
| Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2021Title: Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal. Authors: Rack, J.G.M. / Liu, Q. / Zorzini, V. / Voorneveld, J. / Ariza, A. / Honarmand Ebrahimi, K. / Reber, J.M. / Krassnig, S.C. / Ahel, D. / van der Marel, G.A. / Mangerich, A. / McCullagh, J.S.O. ...Authors: Rack, J.G.M. / Liu, Q. / Zorzini, V. / Voorneveld, J. / Ariza, A. / Honarmand Ebrahimi, K. / Reber, J.M. / Krassnig, S.C. / Ahel, D. / van der Marel, G.A. / Mangerich, A. / McCullagh, J.S.O. / Filippov, D.V. / Ahel, I. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7aks.cif.gz | 529.3 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7aks.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7aks.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7aks_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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| Full document | 7aks_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 7aks_validation.xml.gz | 58.6 KB | Display | |
| Data in CIF | 7aks_validation.cif.gz | 83.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/7aks ftp://data.pdbj.org/pub/pdb/validation_reports/ak/7aks | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7akrC ![]() 7aqmC ![]() 7arwC ![]() 6d36S S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 18 - 361 / Label seq-ID: 4 - 347
NCS ensembles :
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Components
-Protein / Protein/peptide , 2 types, 8 molecules AAACCCEEEGGGBaBDaDFaFHaH
| #1: Protein | Mass: 37796.262 Da / Num. of mol.: 4 / Mutation: E41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRS, ADPRHL2, ARH3 / Production host: ![]() 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: Protein/peptide | Mass: 1096.299 Da / Num. of mol.: 4 / Mutation: E41A / Source method: obtained synthetically Details: chemically sinthesised peptide with ADP-ribosylated serine Source: (synth.) Homo sapiens (human)References: Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, poly(ADP-ribose) glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 5 types, 818 molecules 








| #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-AR6 / [( #7: Water | ChemComp-HOH / | |
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-Details
| 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: 2.51 Å3/Da / Density % sol: 50.91 % |
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| Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: sodium citrate (pH 6.1), 18% (w/v) PEG4000 and 400 mM ammonium acetate |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å |
| Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2019 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
| Reflection | Resolution: 1.86→158.62 Å / Num. obs: 124986 / % possible obs: 99.9 % / Redundancy: 21.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.036 / Rrim(I) all: 0.171 / Net I/σ(I): 12.9 |
| Reflection shell | Resolution: 1.86→1.9 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.824 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5897 / CC1/2: 0.542 / Rpim(I) all: 0.532 / Rrim(I) all: 1.905 / % possible all: 97.7 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 6D36 Resolution: 1.86→97.572 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.175 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.115 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 29.039 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.86→97.572 Å
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| Refine LS restraints |
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United Kingdom, 2items
Citation













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