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- PDB-6oak: Structure of human PARG complexed with JA2131 -

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Basic information

Entry
Database: PDB / ID: 6oak
TitleStructure of human PARG complexed with JA2131
ComponentsPoly(ADP-ribose) glycohydrolase
Keywordshydrolase/hydrolase inhibitor / HYDROLASE / 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 / cytoplasm / cytosol
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-M0M / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBrosey, C.A. / Ahmed, Z. / Warden, S. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA200231-03 United States
CitationJournal: Nat Commun / Year: 2019
Title: Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death.
Authors: Houl, J.H. / Ye, Z. / Brosey, C.A. / Balapiti-Modarage, L.P.F. / Namjoshi, S. / Bacolla, A. / Laverty, D. / Walker, B.L. / Pourfarjam, Y. / Warden, L.S. / Babu Chinnam, N. / Moiani, D. / ...Authors: Houl, J.H. / Ye, Z. / Brosey, C.A. / Balapiti-Modarage, L.P.F. / Namjoshi, S. / Bacolla, A. / Laverty, D. / Walker, B.L. / Pourfarjam, Y. / Warden, L.S. / Babu Chinnam, N. / Moiani, D. / Stegeman, R.A. / Chen, M.K. / Hung, M.C. / Nagel, Z.D. / Ellenberger, T. / Kim, I.K. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
History
DepositionMar 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)61,5672
Polymers61,2241
Non-polymers3431
Water6,485360
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)66.497, 89.333, 94.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61223.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli (E. coli)
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-M0M / (8S)-1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,7,8,9-hexahydro-2H-purin-2-one


Mass: 343.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H21N5O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M (NH3)2SO4, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→37.078 Å / Num. obs: 62296 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1394 / Net I/σ(I): 17.71
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.688 / Num. unique obs: 6098 / CC1/2: 0.431 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B1G

4b1g


Resolution: 1.7→37.078 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 3235 5.2 %
Rwork0.1821 --
obs0.1835 62267 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 22 360 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044066
X-RAY DIFFRACTIONf_angle_d0.7995530
X-RAY DIFFRACTIONf_dihedral_angle_d11.7542428
X-RAY DIFFRACTIONf_chiral_restr0.049607
X-RAY DIFFRACTIONf_plane_restr0.004709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72540.35231220.33872485X-RAY DIFFRACTION98
1.7254-1.75230.371320.29792581X-RAY DIFFRACTION99
1.7523-1.78110.28131250.28032506X-RAY DIFFRACTION100
1.7811-1.81180.29851180.25492535X-RAY DIFFRACTION100
1.8118-1.84470.27451570.24032555X-RAY DIFFRACTION100
1.8447-1.88020.25851500.22732510X-RAY DIFFRACTION100
1.8802-1.91860.29431250.21332588X-RAY DIFFRACTION100
1.9186-1.96030.22881370.19692516X-RAY DIFFRACTION100
1.9603-2.00590.21811440.1882550X-RAY DIFFRACTION100
2.0059-2.05610.23521560.18442524X-RAY DIFFRACTION100
2.0561-2.11160.20991610.16842521X-RAY DIFFRACTION100
2.1116-2.17380.22461320.16462562X-RAY DIFFRACTION100
2.1738-2.24390.20771370.16532577X-RAY DIFFRACTION100
2.2439-2.32410.16871480.16352544X-RAY DIFFRACTION100
2.3241-2.41720.23931360.16222549X-RAY DIFFRACTION100
2.4172-2.52710.20191580.17172548X-RAY DIFFRACTION100
2.5271-2.66030.22861240.17152612X-RAY DIFFRACTION100
2.6603-2.8270.19861310.17562560X-RAY DIFFRACTION100
2.827-3.04510.21961530.1862598X-RAY DIFFRACTION100
3.0451-3.35140.1961620.18112559X-RAY DIFFRACTION100
3.3514-3.83590.19981630.16672618X-RAY DIFFRACTION100
3.8359-4.83120.14421240.15422653X-RAY DIFFRACTION100
4.8312-37.08710.21061400.19762781X-RAY DIFFRACTION100

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