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- PDB-7arw: Structure of human ARH3 E41A bound to alpha-NAD+ and magnesium -

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Basic information

Entry
Database: PDB / ID: 7arw
TitleStructure of human ARH3 E41A bound to alpha-NAD+ and magnesium
ComponentsADP-ribose glycohydrolase ARH3
KeywordsHYDROLASE / ADP-ribose glycohydrolase / ARH3 / human / alpha-NAD+
Function / homology
Function and homology information


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 ...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
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / :
Similarity search - Domain/homology
alpha-Diphosphopyridine nucleotide / ACETATE ION / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsRack, J.G.M. / Zorzini, V. / Ahel, I.
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 26, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribose glycohydrolase ARH3
B: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87922
Polymers75,5932
Non-polymers2,28720
Water13,601755
1
A: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94011
Polymers37,7961
Non-polymers1,14310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
2
B: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94011
Polymers37,7961
Non-polymers1,14310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)44.746, 66.112, 70.055
Angle α, β, γ (deg.)115.800, 94.980, 104.070
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRS, ADPRHL2, ARH3 / Production host: Escherichia coli BL21(DE3) (bacteria)
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, 775 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-8NA / alpha-Diphosphopyridine nucleotide / alpha-NAD


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM ammonium acetate (pH 4.5) and 9% (w/v) PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.31→61.52 Å / Num. obs: 157336 / % possible obs: 95.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.1 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Net I/σ(I): 9.8 / Num. measured all: 1042072
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.6 / Num. measured all: 50580 / Num. unique obs: 7642 / Rpim(I) all: 0.417 / Rrim(I) all: 1.089 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D3A

6d3a


Resolution: 1.31→36.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 7763 4.94 %
Rwork0.166 149520 -
obs0.167 157283 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114 Å2 / Biso mean: 27.42 Å2 / Biso min: 8.33 Å2
Refinement stepCycle: final / Resolution: 1.31→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 148 759 5865
Biso mean--28.71 41.08 -
Num. residues----660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.32490.32722470.33244893514093
1.3249-1.34050.32592460.31224807505393
1.3405-1.35680.31472550.29054901515693
1.3568-1.3740.32132530.29734852510593
1.374-1.39210.30682360.29234904514094
1.3921-1.41120.2652420.26784836507893
1.4112-1.43130.26782560.24354941519794
1.4313-1.45270.26562450.22884869511494
1.4527-1.47540.22552940.20354886518094
1.4754-1.49960.19632510.1944928517994
1.4996-1.52540.21672400.18184895513595
1.5254-1.55320.1872530.17554987524095
1.5532-1.5830.1742450.17014942518795
1.583-1.61530.21282580.16024929518795
1.6153-1.65050.18772370.1665005524295
1.6505-1.68890.18492380.16724995523396
1.6889-1.73110.20972680.17034998526696
1.7311-1.77790.19452860.16674959524596
1.7779-1.83020.20012700.16364974524496
1.8302-1.88930.18422700.16195062533296
1.8893-1.95680.19492700.16865057532796
1.9568-2.03510.18222580.1625009526797
2.0351-2.12780.18452490.1555115536497
2.1278-2.23990.17772560.16185036529297
2.2399-2.38020.17242970.16215067536498
2.3802-2.5640.1692760.15935075535198
2.564-2.82190.17122500.15565136538698
2.8219-3.230.17742550.15665146540199
3.23-4.06860.1492690.13935170543999
4.0686-36.010.15562930.15065146543999
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)
13.0162-0.83551.82453.4526-0.07362.729-0.12720.08750.0301-0.07780.01790.0105-0.06710.04940.11130.1336-0.02840.0250.08750.020.09320.7851-1.348821.2579
23.27230.70742.02432.96630.48422.9801-0.13450.16790.121-0.2084-0.01690.2545-0.2333-0.06390.08330.18710.00630.00170.1280.01170.14115.50833.546121.8808
31.2815-0.19320.34541.96250.53131.7933-0.0824-0.15140.11940.2584-0.0096-0.0557-0.1982-0.05680.06630.2283-0.0057-0.03160.1290.00160.114821.62351.664840.5894
44.42810.2908-1.13192.99690.05085.6990.0088-0.5891-0.11620.59490.09310.12670.2835-0.2520.05020.2965-0.0030.00570.20140.05060.174718.6233-18.638840.8299
50.95620.6560.26942.20560.01960.8117-0.01530.0046-0.0261-0.0318-0.01720.0346-0.0029-0.00160.02590.124-0.00030.00220.12560.00060.12915.6646-9.210323.8478
61.4493-0.26180.80791.4855-0.11351.5968-0.1171-0.05290.00750.07290.0691-0.0561-0.0833-0.03380.06410.10050.00330.00980.1065-0.00450.1137-1.444525.109312.6462
74.38730.22630.03434.95040.80121.6767-0.203-0.05810.44230.04240.1433-0.59-0.6910.78280.06450.2541-0.1393-0.01650.30250.01630.25294.94337.5353-2.7866
81.11450.18580.15191.1818-0.70762.21760.00050.0892-0.007-0.12650.01320.04270.1069-0.0278-0.00620.0912-0.0060.0080.1122-0.00830.1171-5.422319.40350.7743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 18 THROUGH 42 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 43 THROUGH 92 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 93 THROUGH 203 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 204 THROUGH 240 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 241 THROUGH 361 )A0
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 18 THROUGH 224 )B0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 225 THROUGH 254 )B0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 255 THROUGH 362 )B0

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