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- PDB-7l9f: Crystal structure of human ARH3 bound to calcium and ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 7l9f
TitleCrystal structure of human ARH3 bound to calcium and ADP-ribose
ComponentsPoly(ADP-ribose) glycohydrolase ARH3
KeywordsHYDROLASE / ADP-ribose / calcium
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 / 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: 1.75 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

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)159,67016
Polymers157,1124
Non-polymers2,55812
Water21,8701214
1
C: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9174
Polymers39,2781
Non-polymers6393
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)39,9174
Polymers39,2781
Non-polymers6393
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)39,9174
Polymers39,2781
Non-polymers6393
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)39,9174
Polymers39,2781
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.930, 71.473, 115.595
Angle α, β, γ (deg.)93.966, 94.328, 107.408
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
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, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1214 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate buffer pH 4.5, 0.1 M CaCl2, 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: 1.75→67.88 Å / Num. obs: 125732 / % possible obs: 91.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.96 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.117 / Num. unique obs: 12401

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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: 1.75→67.88 Å / SU ML: 0.1512 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 18.5287 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 6170 4.91 %
Rwork0.1494 119520 -
obs0.1512 125690 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10014 0 152 1214 11380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009110339
X-RAY DIFFRACTIONf_angle_d1.096514012
X-RAY DIFFRACTIONf_chiral_restr0.05231573
X-RAY DIFFRACTIONf_plane_restr0.00671820
X-RAY DIFFRACTIONf_dihedral_angle_d7.69856148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.21822230.17823791X-RAY DIFFRACTION88.65
1.77-1.790.21482280.17164012X-RAY DIFFRACTION90.99
1.79-1.810.23642160.17663931X-RAY DIFFRACTION91.26
1.81-1.840.22551890.16713943X-RAY DIFFRACTION90.32
1.84-1.860.21851840.1583937X-RAY DIFFRACTION90.27
1.86-1.890.17332120.15323929X-RAY DIFFRACTION90.75
1.89-1.910.19582000.14923932X-RAY DIFFRACTION90.1
1.91-1.940.1881980.15383896X-RAY DIFFRACTION88.86
1.94-1.970.20551980.15643742X-RAY DIFFRACTION86.33
1.97-20.20291840.15693485X-RAY DIFFRACTION80.32
2-2.040.22252140.15833931X-RAY DIFFRACTION89.66
2.04-2.070.17981870.1584062X-RAY DIFFRACTION94.23
2.07-2.110.20312020.14734128X-RAY DIFFRACTION93.93
2.11-2.160.20512280.14554071X-RAY DIFFRACTION93.58
2.16-2.20.2021900.14874092X-RAY DIFFRACTION94.09
2.2-2.260.18641980.14444113X-RAY DIFFRACTION93.35
2.26-2.310.18532260.14034026X-RAY DIFFRACTION93.14
2.31-2.380.18882120.14274068X-RAY DIFFRACTION93.27
2.38-2.440.18961930.14014050X-RAY DIFFRACTION93.54
2.44-2.520.18512000.14064069X-RAY DIFFRACTION92.95
2.52-2.610.16862060.14334041X-RAY DIFFRACTION92.23
2.61-2.720.19362130.14473930X-RAY DIFFRACTION91.62
2.72-2.840.19142150.14933777X-RAY DIFFRACTION86.5
2.84-2.990.17192100.14594030X-RAY DIFFRACTION91.72
2.99-3.180.19332180.15414145X-RAY DIFFRACTION95.89
3.18-3.430.17891980.14864201X-RAY DIFFRACTION95.71
3.43-3.770.17732110.14814132X-RAY DIFFRACTION94.97
3.77-4.320.16632180.12324061X-RAY DIFFRACTION94.02
4.32-5.440.16792060.13923972X-RAY DIFFRACTION91.02
5.44-67.880.20021930.19374023X-RAY DIFFRACTION92.05
Refinement TLS params.Method: refined / Origin x: 0.138181431273 Å / Origin y: -0.619577538899 Å / Origin z: -0.724915905583 Å
111213212223313233
T0.114991482479 Å20.00863489067359 Å2-0.0148137718862 Å2-0.139102216933 Å20.00762903228536 Å2--0.139347155413 Å2
L0.0366895309426 °20.0131831479601 °2-0.0373623609121 °2-0.0653033143799 °20.0335959410084 °2--0.129641873542 °2
S-0.00540868996521 Å °-0.0158819215954 Å °-0.0107525729663 Å °0.00374195194684 Å °-0.00620955586593 Å °0.00329439967132 Å °-0.00527722008963 Å °-0.00780233931447 Å °0.0109132689389 Å °
Refinement TLS groupSelection details: all

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