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- PDB-6d36: Structure of human ARH3 bound to ADP-ribose and magnesium -

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Basic information

Entry
Database: PDB / ID: 6d36
TitleStructure of human ARH3 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: 1.7 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 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)159,54416
Polymers157,1124
Non-polymers2,43212
Water16,790932
1
C: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8864
Polymers39,2781
Non-polymers6083
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)39,8864
Polymers39,2781
Non-polymers6083
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)39,8864
Polymers39,2781
Non-polymers6083
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)39,8864
Polymers39,2781
Non-polymers6083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.918, 72.330, 115.945
Angle α, β, γ (deg.)83.06, 85.74, 72.04
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39277.961 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.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 932 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
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: 1.7→46.451 Å / Num. obs: 146249 / % possible obs: 96.6 % / Redundancy: 3 % / Net I/σ(I): 21.9
Reflection shellResolution: 1.7→1.7193 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2foz

2foz


Resolution: 1.7→46.451 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 7301 4.99 %
Rwork0.1836 --
obs0.1853 146243 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→46.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10090 0 152 932 11174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110468
X-RAY DIFFRACTIONf_angle_d0.95414129
X-RAY DIFFRACTIONf_dihedral_angle_d7.2596195
X-RAY DIFFRACTIONf_chiral_restr0.0541586
X-RAY DIFFRACTIONf_plane_restr0.0061837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.26462570.23054735X-RAY DIFFRACTION98
1.7193-1.73950.25612390.2114642X-RAY DIFFRACTION98
1.7395-1.76080.25782640.2054758X-RAY DIFFRACTION99
1.7608-1.78310.22972460.20544769X-RAY DIFFRACTION99
1.7831-1.80650.26132450.20494779X-RAY DIFFRACTION99
1.8065-1.83130.24672500.2034606X-RAY DIFFRACTION99
1.8313-1.85740.23062550.19454840X-RAY DIFFRACTION98
1.8574-1.88520.22142380.19464699X-RAY DIFFRACTION98
1.8852-1.91460.24842460.19624631X-RAY DIFFRACTION98
1.9146-1.9460.22882740.19194712X-RAY DIFFRACTION98
1.946-1.97960.24432420.19494604X-RAY DIFFRACTION97
1.9796-2.01560.21632680.19294685X-RAY DIFFRACTION97
2.0156-2.05430.22652770.18144613X-RAY DIFFRACTION96
2.0543-2.09630.24112370.1924482X-RAY DIFFRACTION94
2.0963-2.14180.23252410.1934395X-RAY DIFFRACTION91
2.1418-2.19170.23582470.19424543X-RAY DIFFRACTION96
2.1917-2.24650.21532110.1844803X-RAY DIFFRACTION99
2.2465-2.30720.22872150.18564681X-RAY DIFFRACTION99
2.3072-2.37510.23582440.18294759X-RAY DIFFRACTION99
2.3751-2.45170.24112390.18544708X-RAY DIFFRACTION98
2.4517-2.53940.20252430.18684702X-RAY DIFFRACTION98
2.5394-2.6410.21242510.19074636X-RAY DIFFRACTION96
2.641-2.76120.20842370.18594601X-RAY DIFFRACTION96
2.7612-2.90680.22012470.19034469X-RAY DIFFRACTION94
2.9068-3.08890.20482300.18494097X-RAY DIFFRACTION86
3.0889-3.32730.22882430.18274628X-RAY DIFFRACTION96
3.3273-3.6620.19982180.17514756X-RAY DIFFRACTION98
3.662-4.19160.19062630.15354669X-RAY DIFFRACTION97
4.1916-5.27980.19312360.15774526X-RAY DIFFRACTION94
5.2798-46.46830.20141980.19244414X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -0.11 Å / Origin y: 0.1739 Å / Origin z: -0.183 Å
111213212223313233
T0.0349 Å20.0163 Å20.0168 Å2-0.0834 Å2-0.0053 Å2--0.0791 Å2
L0.0112 °20.0275 °20.023 °2-0.103 °2-0.0422 °2--0.1499 °2
S-0.0108 Å °-0.0119 Å °0.0138 Å °-0.0051 Å °-0.0068 Å °-0.0011 Å °0.0044 Å °0.0224 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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