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- PDB-7p0w: Crystal structure of a trapped Pab-AGOG/double-standed DNA covale... -

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Basic information

Entry
Database: PDB / ID: 7p0w
TitleCrystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing thymine opposite to lesion)
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / AGOG / Pyrococcus abyssi / trapped double-stranded DNA intermediate
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 / molecular replacement / Resolution: 1.12 Å
AuthorsCoste, F. / Goffinont, S. / 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
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 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
Revision 1.3Nov 6, 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: N-glycosylase/DNA lyase
B: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
I: DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6017
Polymers33,3193
Non-polymers2824
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-53 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.776, 71.578, 138.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MPD

21A-489-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 27982.514 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules BI

#2: DNA chain DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')


Mass: 2555.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TTT(PED)TTTCT / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*AP*A)-3')


Mass: 2780.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 413 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MgCl2, Na acetate pH5.0, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.12→45.88 Å / Num. obs: 114280 / % possible obs: 99.4 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.7
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5266 / CC1/2: 0.834

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.71 Å45.88 Å

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Processing

Software
NameVersionClassification
autoPROCdata reduction
PHASER2.8.3phasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OY7

7oy7


Resolution: 1.12→34.65 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.143 5802 5.08 %
Rwork0.1239 108468 -
obs0.1249 114270 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 18.223 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: final / Resolution: 1.12→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 353 46 409 2760
Biso mean--16.96 33.44 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.12-1.130.19831800.17613250343091
1.13-1.140.15551710.16073423359494
1.14-1.160.19711670.15193503367097
1.16-1.170.15982030.14293570377399
1.17-1.190.15412000.132635563756100
1.19-1.20.1581650.126436503815100
1.2-1.220.1481790.119236423821100
1.22-1.240.13852090.116935973806100
1.24-1.260.13172170.113435903807100
1.26-1.280.12612040.105735723776100
1.28-1.30.13251840.108436713855100
1.3-1.320.14691990.110335863785100
1.32-1.350.13421800.10736053785100
1.35-1.380.14741770.106736733850100
1.38-1.410.14391780.114736343812100
1.41-1.440.13641980.106435943792100
1.44-1.480.12041750.103836173792100
1.48-1.520.12551980.102536443842100
1.52-1.560.12472180.102236343852100
1.56-1.610.13212110.104336213832100
1.61-1.670.14112170.107536273844100
1.67-1.740.13072050.113835983803100
1.74-1.810.13211770.118436613838100
1.81-1.910.12791900.121536443834100
1.91-2.030.14261890.121936983887100
2.03-2.190.14351760.120636693845100
2.19-2.410.12941980.119836773875100
2.41-2.750.13542090.126537073916100
2.75-3.470.16832070.132637083915100
3.47-34.650.14762210.141438474068100

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