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- PDB-6o9y: Structure of human PARG complexed with JA2-8 -

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Basic information

Entry
Database: PDB / ID: 6o9y
TitleStructure of human PARG complexed with JA2-8
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 / 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 / carbohydrate metabolic process / nuclear body / 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 / 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-M0V / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)61,5472
Polymers61,2241
Non-polymers3231
Water4,035224
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)44.691, 65.993, 88.591
Angle α, β, γ (deg.)90.00, 95.23, 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-M0V / 7-[(2S)-2-hydroxy-3-(morpholin-4-yl)propyl]-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione


Mass: 323.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
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 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 32438 / % possible obs: 98.4 % / Redundancy: 3.9 % / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.053 Å / Num. unique obs: 2017

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.696 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1712 5 %RANDOM
Rwork0.18229 ---
obs0.18503 32438 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.06 Å2
2--0.29 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 23 224 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0144126
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173644
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.6675597
X-RAY DIFFRACTIONr_angle_other_deg1.0781.6348538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3755497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75921.278227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51515687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
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_it1.8762.5651998
X-RAY DIFFRACTIONr_mcbond_other1.8752.5661999
X-RAY DIFFRACTIONr_mcangle_it2.8563.832491
X-RAY DIFFRACTIONr_mcangle_other2.8563.8312492
X-RAY DIFFRACTIONr_scbond_it2.3252.8082128
X-RAY DIFFRACTIONr_scbond_other2.3252.8092129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5534.1233107
X-RAY DIFFRACTIONr_long_range_B_refined4.98129.6974678
X-RAY DIFFRACTIONr_long_range_B_other4.94129.5484645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 115 -
Rwork0.28 2017 -
obs--83.77 %
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)
10.05880.05140.02040.237-0.22470.446-0.011-0.0159-0.0091-0.0133-0.0325-0.00420.00630.03320.04360.03150.00130.00030.00810.00830.02196.6477-0.225420.0418
20.04480.09340.02980.3888-0.25580.55580.01030.0011-0.0050.0436-0.0186-0.0067-0.0220.03860.00830.0172-0.00190.00260.00380.00550.0246.99742.351620.8283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A450 - 963
2X-RAY DIFFRACTION2A1101 - 1324

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