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- PDB-6o9x: Structure of human PARG complexed with JA2-4 -

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Basic information

Entry
Database: PDB / ID: 6o9x
TitleStructure of human PARG complexed with JA2-4
ComponentsPoly(ADP-ribose) glycohydrolasePoly(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 / 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 / nuclear body / carbohydrate metabolic process / 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 / nuclear body / carbohydrate metabolic process / mitochondrial matrix / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Poly (ADP-ribose) glycohydrolase (PARG), helical domain / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold
Similarity search - Domain/homology
Chem-M0S / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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)61,5492
Polymers61,2241
Non-polymers3251
Water7,368409
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)44.564, 65.786, 88.367
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase / 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-M0S / 1,3-dimethyl-8-{[2-(pyrrolidin-1-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,9-tetrahydro-2H-purin-2-one


Mass: 325.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5OS2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350, 0.1 M PCTP pH 7.5 and 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 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 54208 / % possible obs: 97.2 % / Redundancy: 5.7 % / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.744 Å / Num. unique obs: 3458

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→23.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.113 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19316 2751 5.1 %RANDOM
Rwork0.15577 ---
obs0.1577 51551 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.07 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 21 409 4455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0144147
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173640
X-RAY DIFFRACTIONr_angle_refined_deg1.871.6665629
X-RAY DIFFRACTIONr_angle_other_deg1.1631.6348528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71321.385231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5961533
X-RAY DIFFRACTIONr_chiral_restr0.1260.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
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_it1.8622.2072010
X-RAY DIFFRACTIONr_mcbond_other1.8612.2052008
X-RAY DIFFRACTIONr_mcangle_it2.7863.2982507
X-RAY DIFFRACTIONr_mcangle_other2.7863.32507
X-RAY DIFFRACTIONr_scbond_it2.7162.4722137
X-RAY DIFFRACTIONr_scbond_other2.7152.4732138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0993.6083123
X-RAY DIFFRACTIONr_long_range_B_refined5.46626.2094736
X-RAY DIFFRACTIONr_long_range_B_other5.41225.8554670
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 180 -
Rwork0.242 3458 -
obs--88.8 %
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)
10.06030.0595-0.02120.2009-0.1880.3482-0.0102-0.0186-0.012-0.0046-0.0325-0.0050.00460.03070.04270.00490.00170.00590.01430.00950.02196.8077-0.145319.8681
27.23722.357-3.91380.7678-1.27562.1234-0.1258-0.1124-0.3218-0.0397-0.0352-0.10250.05060.05740.1610.0777-0.00980.02820.01720.0190.0437-1.8153-9.689824.514
30.04890.05220.05840.2914-0.21210.4881-0.0072-0.0089-0.00580.0018-0.0214-0.0032-0.00160.03570.02850.00420.00650.00770.01320.01410.01647.24591.940818.4961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A450 - 963
2X-RAY DIFFRACTION2A1001
3X-RAY DIFFRACTION3A1101 - 1509

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