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- 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 | |||||||||
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![]() | HYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADPRHL2 / ADP-RIBOSYLHYDROLASE LIKE 2 / SER-ADPR / SERINE-ADPR / ADP-RIBOSYL-L-SERINE | |||||||||
Function / homology | ![]() ADP-ribosylserine hydrolase activity / peptidyl-serine ADP-deribosylation / cellular response to superoxide / O-acetyl-ADP-ribose deacetylase activity / 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 / cellular response to superoxide / O-acetyl-ADP-ribose deacetylase activity / 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 / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ariza, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 529.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 58.6 KB | Display | |
Data in CIF | ![]() | 83.3 KB | Display | |
Arichive directory | ![]() ![]() | 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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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() 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.) ![]() 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 ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AR6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AR6.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() Starting 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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