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- PDB-6d3a: Structure of human ARH3 D314E bound to ADP-ribose and magnesium -

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Basic information

Entry
Database: PDB / ID: 6d3a
TitleStructure of human ARH3 D314E bound to ADP-ribose and magnesium
ComponentsPoly(ADP-ribose) glycohydrolase ARH3
KeywordsHYDROLASE / poly(ADP-ribose) hydrolase
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
ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60001013785 Å
AuthorsPourfarjam, Y. / Ventura, J. / Kurinov, I. / Kim, I.K.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition.
Authors: Pourfarjam, Y. / Ventura, J. / Kurinov, I. / Cho, A. / Moss, J. / Kim, I.K.
History
DepositionApr 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Structure summary
Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Poly(ADP-ribose) glycohydrolase ARH3
D: Poly(ADP-ribose) glycohydrolase ARH3
A: Poly(ADP-ribose) glycohydrolase ARH3
B: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,50212
Polymers157,1684
Non-polymers2,3348
Water14,664814
1
C: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8763
Polymers39,2921
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8763
Polymers39,2921
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8763
Polymers39,2921
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8763
Polymers39,2921
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.901, 72.229, 115.906
Angle α, β, γ (deg.)83.008, 85.733, 72.430
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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


Mass: 39291.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRHL2, ARH3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NX46, poly(ADP-ribose) glycohydrolase
#2: 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.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 22% PEG4000, 0.1 M sodium acetate pH 4.5, and 0.1 M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→68.48 Å / Num. obs: 173752 / % possible obs: 95.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.2976613537 Å2 / Net I/σ(I): 17.6
Reflection shellResolution: 1.6→1.618 Å

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Processing

Software
NameVersionClassification
phenix.refine1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60001013785→68.4830190676 Å / SU ML: 0.169369997884 / Cross valid method: FREE R-VALUE / σ(F): 1.99692749806 / Phase error: 20.525211217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198472784025 8616 4.95887746117 %
Rwork0.167047470217 165133 -
obs0.168559378874 173749 95.6172645876 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.821425451 Å2
Refinement stepCycle: LAST / Resolution: 1.60001013785→68.4830190676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10134 0 148 814 11096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067316513228210492
X-RAY DIFFRACTIONf_angle_d0.93868007993514193
X-RAY DIFFRACTIONf_chiral_restr0.04653843887261591
X-RAY DIFFRACTIONf_plane_restr0.005586677349171844
X-RAY DIFFRACTIONf_dihedral_angle_d13.22029895836223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.2727042605372880.249478903865122X-RAY DIFFRACTION89.4214876033
1.6182-1.63720.2601047716662690.2238826732635247X-RAY DIFFRACTION91.2489660877
1.6372-1.65720.2496667667052780.2077116153025386X-RAY DIFFRACTION93.0202003613
1.6572-1.67820.2477970991222850.2086236125265427X-RAY DIFFRACTION94.5695364238
1.6782-1.70030.259543907672780.2030417129625469X-RAY DIFFRACTION95.259406597
1.7003-1.72360.2236721575252890.2073414725985565X-RAY DIFFRACTION95.591116917
1.7236-1.74820.2358562386692610.1983231766985449X-RAY DIFFRACTION95.4211229947
1.7482-1.77430.2557053638243080.2025857724585484X-RAY DIFFRACTION95.5775577558
1.7743-1.8020.2315433505522670.1959722163465562X-RAY DIFFRACTION95.808678501
1.802-1.83150.2242117395532920.1868588903095482X-RAY DIFFRACTION95.8340248963
1.8315-1.86310.20592458393010.1870221620235582X-RAY DIFFRACTION96.0333006856
1.8631-1.8970.2409868478572860.1877911989125493X-RAY DIFFRACTION96.3809206137
1.897-1.93350.2178968768092780.1877844684945538X-RAY DIFFRACTION96.1799239292
1.9335-1.9730.2327342317963200.1800676639525522X-RAY DIFFRACTION96.101332456
1.973-2.01590.2139009374243230.1828914256685523X-RAY DIFFRACTION96.3414634146
2.0159-2.06280.2232763585232710.1824326406295572X-RAY DIFFRACTION96.3873309139
2.0628-2.11440.2235888013412840.1806825570135554X-RAY DIFFRACTION96.8641114983
2.1144-2.17150.1914222672993030.1710821535535514X-RAY DIFFRACTION96.3558058638
2.1715-2.23540.1883298574952800.1621564897495628X-RAY DIFFRACTION96.5201764418
2.2354-2.30760.1813116305642930.1650301199755503X-RAY DIFFRACTION96.7128316369
2.3076-2.39010.1922392362333020.1644709007855611X-RAY DIFFRACTION96.8391745824
2.3901-2.48580.2111731476143050.1620496148755560X-RAY DIFFRACTION96.3687150838
2.4858-2.59890.1896835702512960.1600801383415502X-RAY DIFFRACTION96.3282937365
2.5989-2.73590.1822793021792910.1589727821595479X-RAY DIFFRACTION95.8790295779
2.7359-2.90730.2088219488912890.1657406665485411X-RAY DIFFRACTION93.6883629191
2.9073-3.13180.1955912951862890.1666988206365631X-RAY DIFFRACTION97.512765607
3.1318-3.4470.2019850938882820.1643117462455689X-RAY DIFFRACTION97.6451349141
3.447-3.94570.184013215332540.1455642561165549X-RAY DIFFRACTION97.2189646507
3.9457-4.9710.1525510767032790.1304918360935581X-RAY DIFFRACTION96.1128423815
4.971-68.54580.1893456172092750.179677618075498X-RAY DIFFRACTION95.3741946142
Refinement TLS params.Method: refined / Origin x: -0.06406479104 Å / Origin y: 0.0564808543033 Å / Origin z: -0.0178801849691 Å
111213212223313233
T0.16041621105 Å20.0086354177365 Å20.0142345490045 Å2-0.208105132954 Å2-0.0109359340735 Å2--0.193965953044 Å2
L0.0116417424859 °20.0222999825198 °20.0322971693582 °2-0.106670442947 °2-0.050966330959 °2--0.228684623058 °2
S-0.00812253374783 Å °-0.0132710838423 Å °0.00919798171482 Å °0.00235519823412 Å °-0.00383443488941 Å °-0.00239635026343 Å °0.005823199827 Å °0.0449939376603 Å °0.011238281079 Å °
Refinement TLS groupSelection details: all

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