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- PDB-7p8l: Crystal structure of Pyrococcus abyssi 8-oxoguanine DNA glycosyla... -

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Basic information

Entry
Database: PDB / ID: 7p8l
TitleCrystal structure of Pyrococcus abyssi 8-oxoguanine DNA glycosylase (PabAGOG) in complex with dsDNA containing cytosine opposite to 8-oxoG
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*(8OG)P*TP*TP*TP*CP*T)-3')
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / Pyrococcus abyssi / protein-DNA complex
Function / homology
Function and homology information


oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair
Similarity search - Function
N-glycosylase/DNA lyase-like / N-glycosylase/DNA lyase / N-glycosylase/DNA lyase / DNA glycosylase
Similarity search - Domain/homology
DNA / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCoste, F. / Flament, D. / Castaing, B.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Authors: Franck, C. / Stephane, G. / Julien, C. / Virginie, G. / Martine, G. / Norbert, G. / Fabrice, C. / Didier, F. / Josef, S.M. / Bertrand, C.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: DNA (5'-D(*TP*TP*TP*(8OG)P*TP*TP*TP*CP*T)-3')
I: DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7025
Polymers33,4663
Non-polymers2362
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-20 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.256, 68.811, 140.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-540-

HOH

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Components

#1: Protein N-glycosylase/DNA lyase / 8-oxoguanine DNA glycosylase / AGOG / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 27981.463 Da / Num. of mol.: 1 / Mutation: K142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: PYRAB10170, PAB1695 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UZY0, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*TP*TP*TP*(8OG)P*TP*TP*TP*CP*T)-3')


Mass: 2718.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3')


Mass: 2765.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Na acetate pH 4.5, KCl, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.25→46.17 Å / Num. obs: 83399 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 13.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.5
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4101 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OY7

7oy7


Resolution: 1.25→46.17 Å / SU ML: 0.087 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.8376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.161 4080 4.89 %
Rwork0.1351 79316 -
obs0.1364 83396 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.95 Å2
Refinement stepCycle: LAST / Resolution: 1.25→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 364 16 305 2638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582476
X-RAY DIFFRACTIONf_angle_d0.90453444
X-RAY DIFFRACTIONf_chiral_restr0.0687381
X-RAY DIFFRACTIONf_plane_restr0.0099372
X-RAY DIFFRACTIONf_dihedral_angle_d18.3102958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.15011240.13082697X-RAY DIFFRACTION99.89
1.26-1.280.16311130.12262742X-RAY DIFFRACTION100
1.28-1.30.14581430.11412744X-RAY DIFFRACTION100
1.3-1.310.16351540.1132664X-RAY DIFFRACTION100
1.31-1.330.14511560.11252718X-RAY DIFFRACTION100
1.33-1.350.15011290.11642699X-RAY DIFFRACTION100
1.35-1.370.13911390.11832718X-RAY DIFFRACTION100
1.37-1.390.13591450.11082681X-RAY DIFFRACTION99.96
1.39-1.410.16121430.11262715X-RAY DIFFRACTION100
1.41-1.440.14631500.10722733X-RAY DIFFRACTION100
1.44-1.470.14971340.10732703X-RAY DIFFRACTION100
1.47-1.490.13461500.10672742X-RAY DIFFRACTION100
1.49-1.520.14841190.10352710X-RAY DIFFRACTION100
1.52-1.560.14251370.10342758X-RAY DIFFRACTION99.97
1.56-1.590.15091510.11352703X-RAY DIFFRACTION100
1.59-1.630.13891270.11982735X-RAY DIFFRACTION100
1.63-1.680.16341450.13052712X-RAY DIFFRACTION100
1.68-1.730.17611360.13292748X-RAY DIFFRACTION100
1.73-1.780.16591320.13772752X-RAY DIFFRACTION100
1.78-1.850.15261390.13022718X-RAY DIFFRACTION100
1.85-1.920.1521390.13482746X-RAY DIFFRACTION100
1.92-2.010.14711380.14312756X-RAY DIFFRACTION100
2.01-2.110.16351590.1382729X-RAY DIFFRACTION100
2.11-2.250.15171430.13962739X-RAY DIFFRACTION100
2.25-2.420.15881490.13972745X-RAY DIFFRACTION100
2.42-2.660.18941480.14652754X-RAY DIFFRACTION99.93
2.66-3.050.17841390.15252792X-RAY DIFFRACTION100
3.05-3.840.15721630.14012822X-RAY DIFFRACTION99.93
3.84-46.170.1711360.14322841X-RAY DIFFRACTION97.07

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