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- PDB-7l9i: Crystal structure of human ARH3-D314A bound to magnesium and ADP-... -

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Basic information

Entry
Database: PDB / ID: 7l9i
TitleCrystal structure of human ARH3-D314A bound to magnesium and ADP-ribose
ComponentsADP-ribose glycohydrolase ARH3
KeywordsHYDROLASE / ADP-ribose / calcium
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
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPourfarjam, Y. / Kurinov, I. / Moss, J. / Kim, I.K.
Funding support United States, 1items
OrganizationGrant numberCountry
American Cancer Society133405-RSG-19-200-01-DMC United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 reveals the basis of metal selectivity and different roles for the two magnesium ions.
Authors: Pourfarjam, Y. / Ma, Z. / Kurinov, I. / Moss, J. / Kim, I.K.
History
DepositionJan 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,27012
Polymers156,9364
Non-polymers2,3348
Water15,115839
1
C: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.808, 71.428, 115.803
Angle α, β, γ (deg.)94.033, 94.626, 107.860
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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: 39233.953 Da / Num. of mol.: 4 / Mutation: D314A
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
#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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 839 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate buffer pH 4.5, 0.1 M MgCl2, and 24 % polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→67.64 Å / Num. obs: 112761 / % possible obs: 89.77 % / Redundancy: 1.9 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 11030

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D36

6d36


Resolution: 1.8→67.64 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.183 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 5693 5.05 %
Rwork0.1887 107068 -
obs0.1908 112761 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9986 0 148 839 10973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005610312
X-RAY DIFFRACTIONf_angle_d0.848213988
X-RAY DIFFRACTIONf_chiral_restr0.04381579
X-RAY DIFFRACTIONf_plane_restr0.00471815
X-RAY DIFFRACTIONf_dihedral_angle_d7.42226120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35451600.31113170X-RAY DIFFRACTION80.55
1.82-1.840.38151840.29743641X-RAY DIFFRACTION90.53
1.84-1.860.31642170.28273648X-RAY DIFFRACTION91.63
1.86-1.890.26551970.26363603X-RAY DIFFRACTION90.97
1.89-1.910.3141810.24473626X-RAY DIFFRACTION91.82
1.91-1.940.28021820.22793708X-RAY DIFFRACTION91.62
1.94-1.970.25981950.21283545X-RAY DIFFRACTION91
1.97-20.26191680.20573629X-RAY DIFFRACTION90
2-2.030.22222110.19663601X-RAY DIFFRACTION90.76
2.03-2.060.23791840.19123522X-RAY DIFFRACTION89.34
2.06-2.10.21781750.18783545X-RAY DIFFRACTION88.49
2.1-2.130.25441950.1883520X-RAY DIFFRACTION87.6
2.13-2.180.25121630.18873227X-RAY DIFFRACTION82.06
2.18-2.220.23891810.18243467X-RAY DIFFRACTION86.59
2.22-2.270.20571960.18223710X-RAY DIFFRACTION93.58
2.27-2.320.22441820.17353697X-RAY DIFFRACTION92.75
2.32-2.380.21062010.17143725X-RAY DIFFRACTION92.68
2.38-2.440.20321960.17433601X-RAY DIFFRACTION91.96
2.44-2.510.22162150.17633650X-RAY DIFFRACTION91.61
2.51-2.60.20591870.17493544X-RAY DIFFRACTION89.8
2.6-2.690.22112160.17753519X-RAY DIFFRACTION89.35
2.69-2.80.23821760.18373319X-RAY DIFFRACTION82.22
2.8-2.920.21241970.17983500X-RAY DIFFRACTION89.32
2.92-3.080.22481980.18173731X-RAY DIFFRACTION94.09
3.08-3.270.21151990.18233721X-RAY DIFFRACTION92.83
3.27-3.520.23621880.17523638X-RAY DIFFRACTION92.08
3.52-3.880.19071890.16513565X-RAY DIFFRACTION89.32
3.88-4.440.18611780.14953408X-RAY DIFFRACTION85.16
4.44-5.590.20191910.17533754X-RAY DIFFRACTION94.13
5.59-67.640.25021910.22153534X-RAY DIFFRACTION89

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