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- PDB-4l2h: Structure of a catalytically inactive PARG in complex with a poly... -

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Basic information

Entry
Database: PDB / ID: 4l2h
TitleStructure of a catalytically inactive PARG in complex with a poly-ADP-ribose fragment
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / macrodomain / poly-ADP-ribose glycohydrolase / poly-ADP-ribose
Function / homologyPoly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / carbohydrate metabolic process / Chem-AR6 / Poly(ADP-ribose) glycohydrolase
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBrassington, A. / Dunstan, M.S. / Leys, D.
CitationJournal: Nat Commun / Year: 2013
Title: Visualization of poly(ADP-ribose) bound to PARG reveals inherent balance between exo- and endo-glycohydrolase activities.
Authors: Barkauskaite, E. / Brassington, A. / Tan, E.S. / Warwicker, J. / Dunstan, M.S. / Banos, B. / Lafite, P. / Ahel, M. / Mitchison, T.J. / Ahel, I. / Leys, D.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)57,0043
Polymers55,8851
Non-polymers1,1192
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.928, 75.713, 138.957
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: 55885.043 Da / Num. of mol.: 1 / Mutation: E256Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: I6L8L7, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.46→29.51 Å / Num. all: 97166 / Num. obs: 97166 / % possible obs: 99.6 %

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EPP

4epp


Resolution: 1.46→29.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.809 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17698 5111 5 %RANDOM
Rwork0.13831 ---
all0.14031 97166 --
obs0.14031 97166 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2---0.11 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.46→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 62 462 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223808
X-RAY DIFFRACTIONr_bond_other_d0.0030.022654
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.995150
X-RAY DIFFRACTIONr_angle_other_deg1.2293.0066534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44325.904188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69715757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681513
X-RAY DIFFRACTIONr_chiral_restr0.1520.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024151
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02736
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_it2.451.52224
X-RAY DIFFRACTIONr_mcbond_other0.9431.5898
X-RAY DIFFRACTIONr_mcangle_it3.523619
X-RAY DIFFRACTIONr_scbond_it5.56931584
X-RAY DIFFRACTIONr_scangle_it7.9834.51517
X-RAY DIFFRACTIONr_rigid_bond_restr2.33836462
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 354 -
Rwork0.242 7003 -
obs--97.74 %

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