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- PDB-7kfp: Structure of human PARG complexed with PARG-119 -

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Basic information

Entry
Database: PDB / ID: 7kfp
TitleStructure of human PARG complexed with PARG-119
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex
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-WD7 / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrosey, C.A. / Bommagani, S. / Warden, L.S. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA200231 United States
CitationJournal: Prog.Biophys.Mol.Biol. / Year: 2021
Title: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.
Authors: Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
History
DepositionOct 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)62,0319
Polymers61,0201
Non-polymers1,0118
Water4,576254
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)66.532, 88.660, 94.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61020.375 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) / Strain (production host): Rosett2(DE3)
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-WD7 / N-{[2-(1,3-dimethyl-2-oxo-6-sulfanylidene-1,2,3,6-tetrahydro-7H-purin-7-yl)ethyl]carbamoyl}methanesulfonamide


Mass: 360.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N6O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


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


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


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2019
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.9→29.58 Å / Num. obs: 44680 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08665 / Rpim(I) all: 0.03888 / Rrim(I) all: 0.09518 / Net I/σ(I): 10.52
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6 % / Rmerge(I) obs: 0.6689 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 4419 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.2983 / Rrim(I) all: 0.7339 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B1G

4b1g


Resolution: 1.9→29.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 2260 5.06 %
Rwork0.1746 42414 -
obs0.1757 44674 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 37.574 Å2 / Biso min: 19.56 Å2
Refinement stepCycle: final / Resolution: 1.9→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 86 254 4166
Biso mean--46.84 39.21 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.940.27511320.237726172749
1.94-1.990.22451410.214525952736
1.99-2.040.24931490.203726002749
2.04-2.090.19091340.171626452779
2.09-2.150.18941290.170226182747
2.15-2.220.19421210.163726572778
2.22-2.30.20091430.153226182761
2.3-2.390.19081580.157426022760
2.39-2.50.21831360.15826392775
2.5-2.630.23061320.166126462778
2.63-2.80.20221330.165526572790
2.8-3.020.2081450.179226502795
3.02-3.320.17511500.1826622812
3.32-3.80.19131580.161126632821
3.8-4.780.15081400.158727172857
4.78-29.580.21761590.207328282987
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)
11.48540.9530.17751.26760.25330.4898-0.10130.21110.3074-0.12130.1260.4342-0.132-0.034-0.01690.27370.0012-0.03310.2710.07850.32652.4714-0.4764-10.3864
21.48350.29840.32032.9333-1.09332.0508-0.06920.3671-0.3314-0.48230.20620.00120.16760.0564-0.11870.3198-0.0365-0.03920.3022-0.09860.29598.5874-26.288-18.0935
31.6655-0.35020.40961.9226-0.541.4076-0.05960.0618-0.2204-0.05940.0916-0.03110.02260.0592-0.03540.197-0.02750.01440.2193-0.03210.221915.0888-20.301-5.9687
41.83721.2693-0.15962.45070.05690.2853-0.03910.09090.1766-0.03190.11820.0521-0.1247-0.0005-0.08220.2528-0.00670.0030.23090.0160.207518.45795.8628-8.3083
51.39680.43630.16122.1032-0.44961.2167-0.02560.0135-0.04510.02630.0475-0.0856-0.22860.1242-0.01120.2503-0.02330.00320.2525-0.00990.209117.7661-4.7021-4.6569
61.54290.9704-0.41631.9883-0.61080.3881-0.1995-0.0759-0.0405-0.03680.08730.00940.00850.03930.11730.28130.0032-0.01040.276-0.01270.180118.10043.7149-8.072
72.88780.3501-1.34381.94270.02132.8718-0.00470.32540.2038-0.24610.128-0.0261-0.0796-0.1586-0.14860.3197-0.0391-0.01050.26080.03310.254622.445310.6775-13.3417
82.83370.8751-0.32742.6605-0.47222.0639-0.03130.11790.3155-0.05870.0545-0.1673-0.11490.2097-0.02780.2616-0.0401-0.00830.2151-0.01220.266232.478919.6888-8.9049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 451 through 508 )A451 - 508
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 543 )A509 - 543
3X-RAY DIFFRACTION3chain 'A' and (resid 544 through 688 )A544 - 688
4X-RAY DIFFRACTION4chain 'A' and (resid 689 through 753 )A689 - 753
5X-RAY DIFFRACTION5chain 'A' and (resid 754 through 804 )A754 - 804
6X-RAY DIFFRACTION6chain 'A' and (resid 805 through 837 )A805 - 837
7X-RAY DIFFRACTION7chain 'A' and (resid 838 through 878 )A838 - 878
8X-RAY DIFFRACTION8chain 'A' and (resid 879 through 961 )A879 - 961

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