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- PDB-7kg8: Structure of human PARG complexed with PARG-061 -

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Basic information

Entry
Database: PDB / ID: 7kg8
TitleStructure of human PARG complexed with PARG-061
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain
Similarity search - Domain/homology
CACODYLATE ION / Chem-WDM / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsBrosey, C.A. / Balapiti-Modarage, L.P.F. / Warden, L.S. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA200231 United States
CitationJournal: Prog.Biophys.Mol.Biol. / Year: 2021
Title: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.
Authors: Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
History
DepositionOct 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0949
Polymers61,0961
Non-polymers9978
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.408, 89.201, 93.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61096.492 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-WDM / 1,3-dimethyl-8-{[2-(morpholin-4-yl)-2-oxoethyl]sulfanyl}-6-sulfanylidene-1,3,6,7-tetrahydro-2H-purin-2-one


Mass: 355.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N5O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2019
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→38.33 Å / Num. obs: 103197 / % possible obs: 99.58 % / Redundancy: 7.8 % / Biso Wilson estimate: 22.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06384 / Rpim(I) all: 0.02406 / Rrim(I) all: 0.06836 / Net I/σ(I): 13.49
Reflection shellResolution: 1.43→1.481 Å / Redundancy: 8.1 % / Rmerge(I) obs: 2.646 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 10175 / CC1/2: 0.393 / CC star: 0.751 / Rpim(I) all: 0.9804 / Rrim(I) all: 2.826 / % possible all: 98.92

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B1G

4b1g


Resolution: 1.43→38.33 Å / SU ML: 0.1635 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1923 5155 5 %
Rwork0.1724 97888 -
obs0.1734 103043 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.88 Å2
Refinement stepCycle: LAST / Resolution: 1.43→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 54 434 4397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534125
X-RAY DIFFRACTIONf_angle_d0.86625618
X-RAY DIFFRACTIONf_chiral_restr0.0678615
X-RAY DIFFRACTIONf_plane_restr0.0047720
X-RAY DIFFRACTIONf_dihedral_angle_d14.24161469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.38311420.33433220X-RAY DIFFRACTION98.22
1.45-1.460.32181470.31513225X-RAY DIFFRACTION99.09
1.46-1.480.28281770.29543192X-RAY DIFFRACTION99.47
1.48-1.50.29371630.29043250X-RAY DIFFRACTION99.5
1.5-1.520.28651820.28363200X-RAY DIFFRACTION99.47
1.52-1.540.2791780.27123247X-RAY DIFFRACTION99.45
1.54-1.560.28581570.26513207X-RAY DIFFRACTION99.23
1.56-1.590.27021750.23953211X-RAY DIFFRACTION99.18
1.59-1.610.24291570.22613247X-RAY DIFFRACTION99.65
1.61-1.640.26031630.20643238X-RAY DIFFRACTION99.82
1.64-1.670.23751650.19543257X-RAY DIFFRACTION99.74
1.67-1.70.21871850.19153223X-RAY DIFFRACTION99.94
1.7-1.730.23341650.1853239X-RAY DIFFRACTION99.79
1.73-1.760.20651580.17973264X-RAY DIFFRACTION99.8
1.76-1.80.19841520.18413295X-RAY DIFFRACTION99.86
1.8-1.840.20851730.17353247X-RAY DIFFRACTION99.71
1.84-1.890.19781860.17973222X-RAY DIFFRACTION99.36
1.89-1.940.22022000.16533221X-RAY DIFFRACTION99.77
1.94-20.17321770.15623265X-RAY DIFFRACTION99.77
2-2.060.18421850.14963253X-RAY DIFFRACTION99.94
2.06-2.140.15621730.14753291X-RAY DIFFRACTION99.94
2.14-2.220.17231600.14643273X-RAY DIFFRACTION99.85
2.22-2.320.17811720.14953247X-RAY DIFFRACTION99.77
2.32-2.450.18951930.15753263X-RAY DIFFRACTION99.51
2.45-2.60.16291870.15223289X-RAY DIFFRACTION99.97
2.6-2.80.17221700.15453319X-RAY DIFFRACTION99.89
2.8-3.080.19681450.16843339X-RAY DIFFRACTION99.86
3.08-3.530.17381770.16533297X-RAY DIFFRACTION99.14
3.53-4.440.16411850.14923382X-RAY DIFFRACTION99.75
4.44-38.330.21072060.19423465X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: 17.7408166808 Å / Origin y: -2.71161868583 Å / Origin z: -8.53140189802 Å
111213212223313233
T0.167222879754 Å2-0.00443183997147 Å22.00938382098E-5 Å2-0.187244872091 Å2-0.00217997649119 Å2--0.143434943779 Å2
L0.80703781637 °20.4666571794 °2-0.0715897797595 °2-1.24373934874 °2-0.157944940324 °2--0.212043754815 °2
S-0.0390527333684 Å °0.0697695589672 Å °0.0187199694433 Å °-0.0426989709494 Å °0.0648661880107 Å °-0.014784121251 Å °-0.0445865710981 Å °0.0260259942598 Å °-0.0203121385445 Å °
Refinement TLS groupSelection details: all

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