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- PDB-6oa3: Structure of human PARG complexed with JA2131 -

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Basic information

Entry
Database: PDB / ID: 6oa3
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 / 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-M0M / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStegeman, R.A. / Jones, D.E. / Ellenberger, T. / Kim, I.K. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) 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 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)61,5672
Polymers61,2241
Non-polymers3431
Water4,432246
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)44.675, 65.948, 88.598
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61223.633 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 (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: obtained synthetically / Formula: C13H21N5O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.05 M PCTP pH 7.5, 0.1 M NaCl, 0.15 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 37412 / % possible obs: 97.3 % / Redundancy: 3.8 % / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.949 Å / Num. unique obs: 2326

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.302 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 1983 5 %RANDOM
Rwork0.17835 ---
obs0.18067 37404 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.3 Å2
2---0.31 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 22 246 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0144132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173639
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6675605
X-RAY DIFFRACTIONr_angle_other_deg1.0831.6338529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1845497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75721.255231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011534
X-RAY DIFFRACTIONr_chiral_restr0.0970.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7432.1991998
X-RAY DIFFRACTIONr_mcbond_other1.7422.21999
X-RAY DIFFRACTIONr_mcangle_it2.6793.2852492
X-RAY DIFFRACTIONr_mcangle_other2.6783.2852493
X-RAY DIFFRACTIONr_scbond_it2.212.4282134
X-RAY DIFFRACTIONr_scbond_other2.212.432135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4143.5573114
X-RAY DIFFRACTIONr_long_range_B_refined4.83125.2414645
X-RAY DIFFRACTIONr_long_range_B_other4.78525.1384611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 117 -
Rwork0.251 2326 -
obs--81.92 %
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)
10.04830.059-0.01090.298-0.24180.4179-0.0089-0.0175-0.0012-0.0075-0.03550.00020.00320.04060.04440.02410.0019-0.01330.010.0070.02116.6105-0.209819.9683
20.04980.0982-0.00730.3707-0.12320.5192-0.0107-0.00260.01290.02290.0025-0.01690.00610.0290.00830.01660.003-0.01670.00590.00030.01918.14853.585718.8483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 963
2X-RAY DIFFRACTION2C1 - 248

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