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- PDB-7kg6: Structure of human PARG complexed with PARG-322 -

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Basic information

Entry
Database: PDB / ID: 7kg6
TitleStructure of human PARG complexed with PARG-322
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
Chem-WDG / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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)61,3882
Polymers61,0201
Non-polymers3671
Water5,423301
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)66.585, 88.965, 94.727
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

#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
#2: Chemical ChemComp-WDG / 1-{2-[(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)sulfanyl]ethyl}piperidine-4-carboxylic acid


Mass: 367.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2020
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.96→29.15 Å / Num. obs: 41080 / % possible obs: 99.91 % / Redundancy: 11 % / Biso Wilson estimate: 27.28 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1033 / Rpim(I) all: 0.03248 / Rrim(I) all: 0.1084 / Net I/σ(I): 14.94
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.89 / Num. unique obs: 4054 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.2121 / Rrim(I) all: 0.7243 / % possible all: 100

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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: 1.96→29.15 Å / SU ML: 0.1689 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 2049 4.99 %
Rwork0.1725 39018 -
obs0.1741 41067 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.02 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 25 301 4186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513982
X-RAY DIFFRACTIONf_angle_d0.80485422
X-RAY DIFFRACTIONf_chiral_restr0.0461605
X-RAY DIFFRACTIONf_plane_restr0.0046691
X-RAY DIFFRACTIONf_dihedral_angle_d16.64321404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.26261330.1882553X-RAY DIFFRACTION100
2.01-2.060.23691280.18112567X-RAY DIFFRACTION100
2.06-2.110.1891340.16392579X-RAY DIFFRACTION100
2.11-2.170.2081370.15862556X-RAY DIFFRACTION99.96
2.17-2.240.20511310.1562575X-RAY DIFFRACTION99.96
2.24-2.320.20241670.15052548X-RAY DIFFRACTION99.89
2.32-2.420.23851470.15632564X-RAY DIFFRACTION99.96
2.42-2.530.17431280.15412594X-RAY DIFFRACTION99.89
2.53-2.660.20991430.16072575X-RAY DIFFRACTION100
2.66-2.830.20211440.1652581X-RAY DIFFRACTION99.96
2.83-3.040.2221230.18132630X-RAY DIFFRACTION99.96
3.04-3.350.21661490.1772585X-RAY DIFFRACTION100
3.35-3.830.19621370.16662638X-RAY DIFFRACTION100
3.83-4.830.16371340.15762666X-RAY DIFFRACTION99.93
4.83-29.150.23621140.21452807X-RAY DIFFRACTION99.86
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)
11.858628500432.057900114060.4170275762782.684819424190.7480033620080.290145527796-0.03265776181530.1308150443210.540829000461-0.06777514250350.03200160179040.627777175058-0.130569576333-0.01053201996710.00725492645080.2701882019470.0176956579173-0.01097949366880.2433941797360.05755673218860.3875741842174.027077397456.69540556621-6.46131469015
22.21071138906-0.3260777294850.7427398748921.05664445985-0.4661603019821.093867891240.01435301967730.0941975664819-0.461128354922-0.08799164002730.1088097644260.1127853998090.1205047039760.00565572432648-0.1325825944740.197041610658-0.01818736056540.001451951991110.184816104729-0.05452762019780.29269327592712.3925663922-25.6698393988-7.6055268041
31.783488853270.1587415675340.4176290677562.01442782672-0.4617869323761.24248036078-0.04842953534830.221967878182-0.163063442958-0.1307690973360.0378997799572-0.0969336505509-0.009886259808880.1020898259270.02239425285520.169312458517-0.021931127273-0.0006102887395350.190260877587-0.02824678066140.18137771304813.9962587006-15.2368650121-10.0428288711
41.94936681711.42811659152-0.2339607934592.54415520891-0.07373210875140.0326839040653-0.04212651168460.1439219139030.191134347902-0.07957740913340.1126278984930.0603608442839-0.0584887071595-0.029350013488-0.08113968967210.2403636818560.004513281191060.006220728590020.217902198560.01367497308510.21159165991518.52535068875.77629660001-8.37668710158
52.112106970250.6895775868940.07506560488042.8859980278-0.7467807336251.85879547396-0.0235668247497-0.0589815209792-0.05434297775420.0340132430663-0.00304445954758-0.0949440881886-0.1427925889930.213895321480.01470477739190.161065321034-0.0218288113437-0.005814372165670.190097850293-0.01061238863650.16412569002817.8689150299-4.85335278467-4.6384960275
63.356217898441.47323966191-0.8044142163072.12239341505-0.6424899898410.784240128255-0.204062090601-0.1369064349550.167801945785-0.1096740326980.1035032788940.09236851061060.0229616972010.06565958795880.1261492366530.2600162574540.0013042205907-0.003225516937670.218759911985-0.01101235612850.19174496879618.15864596623.63509295998-7.99538557033
72.796818499010.829956462764-0.3570450081442.02544078558-0.4744725587351.71382368853-0.01276892663480.1515276401870.319696541422-0.09014149373340.0696963645789-0.0766681464125-0.08876261311980.0872077254245-0.04933239850110.260862560978-0.0216267626452-0.003118287733740.1748521853050.01864630031760.24092244720129.115808490817.0901331347-10.1300628485
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 493 )451 - 4931 - 43
22chain 'A' and (resid 494 through 601 )494 - 60144 - 141
33chain 'A' and (resid 602 through 688 )602 - 688142 - 228
44chain 'A' and (resid 689 through 753 )689 - 753229 - 293
55chain 'A' and (resid 754 through 804 )754 - 804294 - 344
66chain 'A' and (resid 805 through 837 )805 - 837345 - 377
77chain 'A' and (resid 838 through 962 )838 - 962378 - 498

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