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- PDB-6hh6: Human poly(ADP-ribose) glycohydrolase in complex with ADP-HPM -

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Basic information

Entry
Database: PDB / ID: 6hh6
TitleHuman poly(ADP-ribose) glycohydrolase in complex with ADP-HPM
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / PARG / ADP-HPM
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 / cytoplasm / cytosol
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-A3R / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAriza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2018
Title: (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.
Authors: Rack, J.G.M. / Ariza, A. / Drown, B.S. / Henfrey, C. / Bartlett, E. / Shirai, T. / Hergenrother, P.J. / Ahel, I.
History
DepositionAug 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)61,8556
Polymers60,9441
Non-polymers9115
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-51 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.316, 90.875, 95.276
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
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-A3R / Adenosine Diphosphate (Hydroxymethyl)pyrrolidine monoalcohol


Mass: 526.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N6O11P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.85→54.09 Å / Num. obs: 50546 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.064 / Rrim(I) all: 0.239 / Net I/σ(I): 10
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.674 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3055 / CC1/2: 0.597 / Rpim(I) all: 1.15 / Rrim(I) all: 2.916 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A7R

5a7r


Resolution: 1.85→54.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.491 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20027 2408 4.8 %RANDOM
Rwork0.16595 ---
obs0.16759 48074 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å2-0 Å2
2--0.71 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.85→54.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 54 505 4657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0144374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173868
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6815957
X-RAY DIFFRACTIONr_angle_other_deg1.0151.6359119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37420.952252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64715765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0791540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
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_it1.2411.5782059
X-RAY DIFFRACTIONr_mcbond_other1.241.5762058
X-RAY DIFFRACTIONr_mcangle_it2.0732.3562580
X-RAY DIFFRACTIONr_mcangle_other2.0732.3592581
X-RAY DIFFRACTIONr_scbond_it1.5291.7822315
X-RAY DIFFRACTIONr_scbond_other1.4881.7462297
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4212.5423334
X-RAY DIFFRACTIONr_long_range_B_refined5.83919.0934930
X-RAY DIFFRACTIONr_long_range_B_other5.6718.2844815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 179 -
Rwork0.298 3474 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 18.167 Å / Origin y: 2.775 Å / Origin z: 8.477 Å
111213212223313233
T0.0153 Å20.0008 Å2-0.0112 Å2-0.0079 Å2-0.0076 Å2--0.0673 Å2
L0.7528 °2-0.4157 °2-0.1102 °2-1.3659 °2-0.0229 °2--0.339 °2
S-0.0279 Å °-0.0507 Å °0.0037 Å °0.0367 Å °0.0484 Å °-0.0187 Å °0.0471 Å °0.0213 Å °-0.0205 Å °

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