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- PDB-7akr: Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7akr
TitleHuman ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with ADP-ribose dimer
ComponentsADP-ribose glycohydrolase ARH3
KeywordsHYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADPRHL2 / ADP-RIBOSYLHYDROLASE LIKE 2 / SER-ADPR / SERINE-ADPR
Function / homology
Function and homology information


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
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily
Similarity search - Domain/homology
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAriza, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
Wellcome Trust210634 United Kingdom
CitationJournal: Nat Commun / Year: 2021
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
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: ADP-ribose glycohydrolase ARH3
BBB: ADP-ribose glycohydrolase ARH3
CCC: ADP-ribose glycohydrolase ARH3
DDD: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,04240
Polymers151,1854
Non-polymers5,85736
Water7,873437
1
AAA: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43313
Polymers37,7961
Non-polymers1,63712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1238
Polymers37,7961
Non-polymers1,3277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,27410
Polymers37,7961
Non-polymers1,4789
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2129
Polymers37,7961
Non-polymers1,4168
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.620, 91.600, 91.090
Angle α, β, γ (deg.)90.000, 105.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

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

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
221BBBB
332AAAA
442CCCC
553AAAA
663DDDD
774BBBB
884CCCC
995BBBB
10105DDDD
11116CCCC
12126DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
ADP-ribose glycohydrolase ARH3 / ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / Poly(ADP-ribose) glycohydrolase ...ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / Poly(ADP-ribose) glycohydrolase ARH3 / [Protein ADP-ribosylarginine] hydrolase-like protein 2 / [Protein ADP-ribosylserine] hydrolase


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: 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

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Non-polymers , 5 types, 473 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM TrisHCl (pH 8.5), 20% (w/v) PEG4000 and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.95→70.631 Å / Num. obs: 99860 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.061 / Rrim(I) all: 0.083 / Net I/σ(I): 7.9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1.535 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7382 / CC1/2: 0.503 / Rpim(I) all: 0.638 / Rrim(I) all: 1.665

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D36

6d36


Resolution: 1.95→70.631 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.186 / SU B: 10.579 / SU ML: 0.126 / Average fsc free: 0.8994 / Average fsc work: 0.908 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2106 4757 4.765 %
Rwork0.187 95081 -
all0.188 --
obs-99838 99.881 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.353 Å20 Å20.917 Å2
2---1.291 Å2-0 Å2
3---0.374 Å2
Refinement stepCycle: LAST / Resolution: 1.95→70.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10351 0 327 437 11115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311015
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710074
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.64414856
X-RAY DIFFRACTIONr_angle_other_deg1.3471.57823205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71851379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94322.522571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.152151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0861570
X-RAY DIFFRACTIONr_chiral_restr0.0710.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022484
X-RAY DIFFRACTIONr_nbd_refined0.20.22360
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.28831
X-RAY DIFFRACTIONr_nbtor_refined0.1570.25447
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2407
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.228
X-RAY DIFFRACTIONr_nbd_other0.2010.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3320.215
X-RAY DIFFRACTIONr_mcbond_it1.5153.0655459
X-RAY DIFFRACTIONr_mcbond_other1.5153.0655458
X-RAY DIFFRACTIONr_mcangle_it2.4714.5876824
X-RAY DIFFRACTIONr_mcangle_other2.4714.5886825
X-RAY DIFFRACTIONr_scbond_it1.9343.3775556
X-RAY DIFFRACTIONr_scbond_other1.9343.3775557
X-RAY DIFFRACTIONr_scangle_it3.1974.998021
X-RAY DIFFRACTIONr_scangle_other3.1974.998022
X-RAY DIFFRACTIONr_lrange_it4.74136.08712312
X-RAY DIFFRACTIONr_lrange_other4.7436.08712310
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0510904
X-RAY DIFFRACTIONr_ncsr_local_group_20.0660.0511256
X-RAY DIFFRACTIONr_ncsr_local_group_30.0590.0511051
X-RAY DIFFRACTIONr_ncsr_local_group_40.0580.0511018
X-RAY DIFFRACTIONr_ncsr_local_group_50.0630.0510993
X-RAY DIFFRACTIONr_ncsr_local_group_60.0640.0511054
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.073990.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.073990.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.06650.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.06650.05008
35AAAX-RAY DIFFRACTIONLocal ncs0.059270.05008
36DDDX-RAY DIFFRACTIONLocal ncs0.059270.05008
47BBBX-RAY DIFFRACTIONLocal ncs0.057930.05008
48CCCX-RAY DIFFRACTIONLocal ncs0.057930.05008
59BBBX-RAY DIFFRACTIONLocal ncs0.063020.05008
510DDDX-RAY DIFFRACTIONLocal ncs0.063020.05008
611CCCX-RAY DIFFRACTIONLocal ncs0.064350.05008
612DDDX-RAY DIFFRACTIONLocal ncs0.064350.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.323510.30270260.30373770.7520.7521000.289
2.001-2.0550.2773590.28167990.28171610.8120.82399.95810.262
2.055-2.1150.2873270.26466620.26569920.8290.84699.95710.243
2.115-2.180.2653240.24364430.24467710.870.88599.94090.218
2.18-2.2510.2523270.23162350.23265710.8920.89399.8630.203
2.251-2.330.2383100.21660090.21763330.9050.91199.77890.187
2.33-2.4180.2472860.2158430.21261530.9070.92399.60990.18
2.418-2.5170.2282650.19756050.19858930.9290.93699.60970.171
2.517-2.6290.2162680.18154380.18357080.9370.94299.9650.162
2.629-2.7570.2222500.17851610.1854120.9330.94499.98150.163
2.757-2.9060.2132460.17348740.17551220.9430.9599.9610.163
2.906-3.0810.2112370.18246820.18349210.9380.94599.95940.173
3.081-3.2940.2272550.1843140.18345710.9320.94999.95620.179
3.294-3.5570.1862080.17240610.17242700.9550.95799.97660.175
3.557-3.8960.1751830.16237660.16339530.9640.96599.89880.173
3.896-4.3540.181850.14934210.15136120.9620.96999.83390.168
4.354-5.0240.1741380.15330130.15431560.9720.97499.84160.175
5.024-6.1450.1941130.20225770.20126920.9620.95999.92570.229
6.145-8.6580.196880.17419960.17520840.9590.9621000.208
8.658-70.6310.161370.18211560.18112030.9740.9799.16870.221
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27890.0887-0.04250.86530.14130.28980.0434-0.006-0.0161-0.0226-0.04740.0152-0.0051-0.00380.0040.07350.0105-0.00430.13690.00480.178537.627-6.78952.3395
21.1665-0.33-0.19770.5702-0.03310.2306-0.0308-0.0953-0.0007-0.10390.027-0.06570.0384-0.0360.00380.03020.01170.00340.14410.00570.214-6.8455-12.25343.9121
30.28590.0473-0.41460.3668-0.61421.5447-0.0343-0.0303-0.0035-0.0529-0.0249-0.02380.114-0.03250.05920.10860.0078-0.00280.14180.04010.121136.7601-31.825740.1794
40.6111-0.01020.2230.147-0.22460.98170.00250.09420.2058-0.0226-0.1158-0.00030.06780.08990.11330.0085-0.005-0.01990.21270.14220.2438-5.4357-27.889744.93
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA18 - 361
2X-RAY DIFFRACTION1ALLAaA401
3X-RAY DIFFRACTION1ALLAbA402
4X-RAY DIFFRACTION1ALLAcA403
5X-RAY DIFFRACTION1ALLAdA404
6X-RAY DIFFRACTION1ALLAeA405
7X-RAY DIFFRACTION1ALLAfA406
8X-RAY DIFFRACTION1ALLAgA407
9X-RAY DIFFRACTION1ALLAhA408
10X-RAY DIFFRACTION1ALLAiA409
11X-RAY DIFFRACTION1ALLAjA410
12X-RAY DIFFRACTION1ALLAkA411
13X-RAY DIFFRACTION1ALLAlA412
14X-RAY DIFFRACTION1ALLAmA501 - 678
15X-RAY DIFFRACTION2ALLBBB18 - 361
16X-RAY DIFFRACTION2ALLBaB401
17X-RAY DIFFRACTION2ALLBbB402
18X-RAY DIFFRACTION2ALLBcB403
19X-RAY DIFFRACTION2ALLBdB404
20X-RAY DIFFRACTION2ALLBeB405
21X-RAY DIFFRACTION2ALLBfB406
22X-RAY DIFFRACTION2ALLBgB407
23X-RAY DIFFRACTION2ALLBhB501 - 583
24X-RAY DIFFRACTION3ALLCCC18 - 361
25X-RAY DIFFRACTION3ALLCaC401
26X-RAY DIFFRACTION3ALLCbC402
27X-RAY DIFFRACTION3ALLCcC403
28X-RAY DIFFRACTION3ALLCdC404
29X-RAY DIFFRACTION3ALLCeC406
30X-RAY DIFFRACTION3ALLCfC407
31X-RAY DIFFRACTION3ALLCgC408
32X-RAY DIFFRACTION3ALLChC409
33X-RAY DIFFRACTION3ALLCiC410
34X-RAY DIFFRACTION3ALLCjC501 - 614
35X-RAY DIFFRACTION4ALLDDD18 - 361
36X-RAY DIFFRACTION4ALLDaD401
37X-RAY DIFFRACTION4ALLDbD402
38X-RAY DIFFRACTION4ALLDcD403
39X-RAY DIFFRACTION4ALLDdD404
40X-RAY DIFFRACTION4ALLDeD405
41X-RAY DIFFRACTION4ALLDfD406
42X-RAY DIFFRACTION4ALLDgD407
43X-RAY DIFFRACTION4ALLDhD408
44X-RAY DIFFRACTION4ALLDiD501 - 562

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