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- PDB-6hmm: POLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00013907 -

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Basic information

Entry
Database: PDB / ID: 6hmm
TitlePOLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00013907
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / COMPETITIVE INHIBITOR / PARG
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 / 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-7JB / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTucker, J.A. / Brassington, C. / Hassall, G.
CitationJournal: J.Med.Chem. / Year: 2018
Title: Cell-Active Small Molecule Inhibitors of the DNA-Damage Repair Enzyme Poly(ADP-ribose) Glycohydrolase (PARG): Discovery and Optimization of Orally Bioavailable Quinazolinedione Sulfonamides.
Authors: Waszkowycz, B. / Smith, K.M. / McGonagle, A.E. / Jordan, A.M. / Acton, B. / Fairweather, E.E. / Griffiths, L.A. / Hamilton, N.M. / Hamilton, N.S. / Hitchin, J.R. / Hutton, C.P. / James, D.I. ...Authors: Waszkowycz, B. / Smith, K.M. / McGonagle, A.E. / Jordan, A.M. / Acton, B. / Fairweather, E.E. / Griffiths, L.A. / Hamilton, N.M. / Hamilton, N.S. / Hitchin, J.R. / Hutton, C.P. / James, D.I. / Jones, C.D. / Jones, S. / Mould, D.P. / Small, H.F. / Stowell, A.I.J. / Tucker, J.A. / Waddell, I.D. / Ogilvie, D.J.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 24, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)61,8708
Polymers60,9761
Non-polymers8947
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-31 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.081, 90.367, 95.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 60976.258 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A
Source method: isolated from a genetically manipulated source
Details: Cysteines 268 and 500 have become singly oxidised during purification/ crystallisation (ie microheterogeneity)
Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

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Non-polymers , 5 types, 532 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-7JB / ~{N}-~{tert}-butyl-9,10-bis(oxidanylidene)anthracene-2-sulfonamide


Mass: 343.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Mix purified protein in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT at 7.5 mg/mL with a precipitant consisting of 28% PEG-3350, 0.2 M magnesium chloride, 0.1 M PCTP (0.04 M sodium propionate, ...Details: Mix purified protein in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT at 7.5 mg/mL with a precipitant consisting of 28% PEG-3350, 0.2 M magnesium chloride, 0.1 M PCTP (0.04 M sodium propionate, 0.02 M sodium cacodylate, 0.04 M Bis-Tris propane) pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2010 / Details: Rigaku VariMaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→95.41 Å / Num. obs: 45150 / % possible obs: 95.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2 / Num. unique all: 2509 / % possible all: 78.3

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A0D

4a0d


Resolution: 1.9→27.8 Å / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 2246 5.09 %RANDOM
Rwork0.2012 ---
obs0.2041 44100 95.7 %-
Displacement parametersBiso mean: 29.59 Å2
Baniso -1Baniso -2Baniso -3
1-4.0857 Å20 Å20 Å2
2---1.0638 Å20 Å2
3----3.0219 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 55 525 4642
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONBOND LENGTHS0.014258HARMONIC2
X-RAY DIFFRACTIONBOND ANGLES1.065787HARMONIC2
X-RAY DIFFRACTIONPEPTIDE OMEGA TORSION ANGLES3.21SINUSOIDAL2
X-RAY DIFFRACTIONOTHER TORSION ANGLES16.86SINUSOIDAL2
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.4276 113 4.5 %
Rwork0.3475 2396 -
obs--95.03 %

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