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- PDB-7kg1: Structure of human PARG complexed with PARG-002 -

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Basic information

Entry
Database: PDB / ID: 7kg1
TitleStructure of human PARG complexed with PARG-002
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 activity / poly(ADP-ribose) glycohydrolase / 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 activity / poly(ADP-ribose) glycohydrolase / 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-WDD / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 15, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,44314
Polymers61,0201
Non-polymers1,42213
Water5,459303
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)66.463, 88.964, 95.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61020.375 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 , 6 types, 316 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-WDD / 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione


Mass: 308.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.7 %
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: Feb 6, 2020
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: 1.65→38.66 Å / Num. obs: 68294 / % possible obs: 99.74 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.99 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05614 / Rpim(I) all: 0.01608 / Rrim(I) all: 0.05845 / Net I/σ(I): 24.76
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.655 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 6747 / CC1/2: 0.745 / CC star: 0.924 / Rpim(I) all: 0.4605 / Rrim(I) all: 1.719 / % possible all: 99.69

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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: 1.65→38.66 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 3407 4.99 %
Rwork0.1741 64868 -
obs0.1753 68275 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.24 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 80 303 4259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01384087
X-RAY DIFFRACTIONf_angle_d1.10865566
X-RAY DIFFRACTIONf_chiral_restr0.0724612
X-RAY DIFFRACTIONf_plane_restr0.0087707
X-RAY DIFFRACTIONf_dihedral_angle_d14.29361440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.33761360.27082668X-RAY DIFFRACTION99.75
1.67-1.70.28921500.25922662X-RAY DIFFRACTION99.68
1.7-1.730.25831210.24282672X-RAY DIFFRACTION99.61
1.73-1.750.25591610.22862669X-RAY DIFFRACTION99.86
1.75-1.780.2671400.22062675X-RAY DIFFRACTION99.75
1.78-1.820.24991440.21742654X-RAY DIFFRACTION99.4
1.82-1.850.23851390.19192692X-RAY DIFFRACTION99.86
1.85-1.890.2321400.18132644X-RAY DIFFRACTION99.86
1.89-1.930.21311330.17272680X-RAY DIFFRACTION99.79
1.93-1.970.20871290.16852717X-RAY DIFFRACTION99.82
1.97-2.020.21281330.15922697X-RAY DIFFRACTION99.93
2.02-2.080.18251420.15992668X-RAY DIFFRACTION99.89
2.08-2.140.161270.15012712X-RAY DIFFRACTION99.72
2.14-2.210.17411450.15542670X-RAY DIFFRACTION99.29
2.21-2.290.16811300.15092706X-RAY DIFFRACTION99.86
2.29-2.380.20811460.16092683X-RAY DIFFRACTION99.86
2.38-2.490.19391270.16072720X-RAY DIFFRACTION99.72
2.49-2.620.20271380.16552721X-RAY DIFFRACTION99.9
2.62-2.780.20131790.16392668X-RAY DIFFRACTION99.65
2.78-30.17781460.17282713X-RAY DIFFRACTION99.58
3-3.30.2331430.17432740X-RAY DIFFRACTION99.93
3.3-3.780.17731680.16482732X-RAY DIFFRACTION100
3.78-4.760.16581370.15432798X-RAY DIFFRACTION99.73
4.76-38.660.21341530.20892907X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.436145356073.133373785422.308357978513.693923635562.978864320173.888424115040.0644353228519-0.1444184121420.530365631425-0.193046514807-0.05459072582050.63096599755-0.207754113862-0.374771106574-0.01797542383590.3055279092480.0177760480011-0.03031257454320.2355188936770.09198702235560.458719872378.8561364713112.6523225474-4.17374614202
22.48500013883-0.3307537895430.6343591067661.39019497355-0.5021468680160.72101450061-0.04034417123630.15766368545-0.422699032609-0.1467335186720.1361473593880.1251186255110.08791300798670.0439419804183-0.1010620291540.226653185605-0.02419311875690.01301279658360.219637868217-0.04389554913120.28251158489110.2321017268-23.2635597228-7.62632415539
31.440755193220.862947936627-0.03168537529842.05581194863-0.04631663553480.126041830634-0.1050747409630.269044330537-0.0233522219074-0.2579937596140.1439407011080.0087741501885-0.04696843147970.0191219467704-0.04448339241710.241275742371-0.02204029245220.002749573627270.261554590247-0.006518974410630.18266113230314.7724803697-8.00680081854-10.163915533
42.454073768211.15646805596-0.1011250598032.58792567563-0.4223596507950.400944295339-0.0726106868880.06441700501540.001400873691-0.06160740269550.100023477348-0.0613330451369-0.08723085031630.0396853641145-0.02526216493320.227900963802-0.0122665030588-0.0008834274131290.220684161643-0.01509021784880.17782741727318.4324292964-1.34584357876-5.79298246875
53.475110539291.4489508306-0.7222504389322.89630165461-0.7270581158492.08319099401-0.06134176530220.2537801576770.412230309888-0.160521002870.105487812621-0.068879664498-0.07985365864960.051636335814-0.03759224947190.262893599563-0.0243801843143-0.001963775389680.2126021057450.03812207043910.2624344366829.318601975117.0493421253-10.2394378329
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 451 through 479 )451 - 4791 - 29
22chain 'A' and (resid 480 through 601 )480 - 60130 - 140
33chain 'A' and (resid 602 through 725 )602 - 725141 - 265
44chain 'A' and (resid 726 through 837 )726 - 837266 - 377
55chain 'A' and (resid 838 through 962 )838 - 962378 - 505

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