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- PDB-4a0d: Structure of unliganded human PARG catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4a0d
TitleStructure of unliganded human PARG catalytic domain
ComponentsPOLY(ADP-RIBOSE) GLYCOHYDROLASE
KeywordsHYDROLASE
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 / base-excision repair, gap-filling / regulation of DNA repair / 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 / base-excision repair, gap-filling / regulation of DNA repair / carbohydrate metabolic process / nuclear body / mitochondrial matrix / mitochondrion / 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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBrassington, C. / Ellston, J. / Hassall, G. / Holdgate, G. / McAlister, M. / Overman, R. / Smith, G. / Tucker, J.A. / Watson, M.
CitationJournal: Plos One / Year: 2012
Title: Structures of the Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by Adp-Hpd Derivatives.
Authors: Tucker, J.A. / Bennett, N. / Brassington, C. / Durant, S.T. / Hassall, G. / Holdgate, G. / Mcalister, M. / Nissink, J.W.M. / Truman, C. / Watson, M.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references / Structure summary
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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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)61,7298
Polymers60,9441
Non-polymers7857
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.062, 90.505, 95.169
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: 60944.258 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 448-976 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-6HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 616 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 617 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 616 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 617 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 618 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 688 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 689 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 690 TO ALA
Has protein modificationN
Sequence detailsSIX MUTATIONS INTRODUCED TO IMPROVE CRYSTALLISABILITY K617A,Q618A,K619A,E688A,K689A,K690A

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Description: STRUCTURE SOLVED BY MOLECULAR REPLACEMENT USING COORDINATES FROM SEMET MAD DETERMINATION IN ALTERNATIVE SPACE GROUP
Crystal growDetails: 25% PEG 3350, 36.4MM PCTP 4, 63.6MM PCTP 10, 0.2M MG(SO4)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→46.89 Å / Num. obs: 57354 / % possible obs: 97.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.954 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 2906 5.1 %RANDOM
Rwork0.16463 ---
obs0.16624 54406 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.652 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--1.67 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 42 411 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224400
X-RAY DIFFRACTIONr_bond_other_d0.0010.023031
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9595994
X-RAY DIFFRACTIONr_angle_other_deg2.19437334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8345546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14722.885208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831539
X-RAY DIFFRACTIONr_chiral_restr0.0930.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
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_it0.8421.52657
X-RAY DIFFRACTIONr_mcbond_other0.2291.51060
X-RAY DIFFRACTIONr_mcangle_it1.54424313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.39431743
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8864.51681
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 192 -
Rwork0.254 3937 -
obs--95.51 %
Refinement TLS params.Method: refined / Origin x: 17.9449 Å / Origin y: 2.8709 Å / Origin z: 8.4732 Å
111213212223313233
T0.034 Å20.0024 Å2-0.0108 Å2-0.0449 Å2-0.0087 Å2--0.0054 Å2
L0.5237 °2-0.2064 °2-0.0686 °2-0.9227 °2-0.0418 °2--0.2103 °2
S-0.0173 Å °-0.0718 Å °0.006 Å °0.0406 Å °0.0299 Å °-0.0241 Å °0.0329 Å °0.0112 Å °-0.0126 Å °

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