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- PDB-7oy7: Crystal structure of a trapped Pab-AGOG/double-standed DNA covale... -

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Basic information

Entry
Database: PDB / ID: 7oy7
TitleCrystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing cytosine opposite to lesion)
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*CP*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 / 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: 1.7 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 23, 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 20, 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*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4224
Polymers33,3043
Non-polymers1181
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-17 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.599, 71.832, 138.535
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-515-

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: 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
#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 / 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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MgCl2, Na acetate pH 5.0, 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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→46.18 Å / Num. obs: 33127 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10787 / CC1/2: 0.722

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OUE

7oue


Resolution: 1.7→45.87 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1657 5.02 %
Rwork0.1663 31373 -
obs0.1683 33030 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.85 Å2 / Biso mean: 32.938 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 1.7→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 352 8 280 2584
Biso mean--24.05 39.16 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.38161220.32592568269099
1.75-1.810.32171490.290325762725100
1.81-1.870.32261440.253725722716100
1.87-1.950.29261360.223825792715100
1.95-2.030.26041350.184225872722100
2.03-2.140.25191370.166326002737100
2.14-2.280.20941340.163725712705100
2.28-2.450.20721380.166426272765100
2.45-2.70.2541380.163526212759100
2.7-3.090.1871380.166426402778100
3.09-3.890.17181410.145926702811100
3.89-45.870.15461450.138727622907100
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)
11.1858-0.32640.20095.0372-0.46850.56770.06980.045-0.1420.0097-0.06590.14270.0223-0.0488-0.01530.1915-0.00920.01460.2333-0.01780.2276-7.7241-26.3789-28.5077
23.1659-0.6109-0.65761.6909-1.21353.28740.01420.0070.09790.05110.01-0.0471-0.1591-0.0882-0.0360.227-0.0025-0.01870.2029-0.02010.2306-11.5429-7.3879-19.2062
31.0967-0.6907-0.97092.2265-0.47332.73170.0765-0.26770.08110.22830.04210.0247-0.1634-0.2016-0.1040.23820.0025-0.00380.1956-0.00490.1799-10.7264-7.6322-10.7316
40.5404-0.1053-0.06531.05470.19141.63710.0008-0.0776-0.09340.06330.0025-0.15390.06970.07850.00750.2058-0.0188-0.02510.25240.01210.28910.7679-19.5904-17.5758
53.3451.89970.07176.54840.06933.93520.129-0.2529-0.0931-0.2714-0.07460.23030.34-0.1835-0.07880.2749-0.0670.02870.30560.00260.265-15.9641-35.6376-12.0327
64.86120.6637-1.0864.3334-1.02754.69460.173-0.2183-0.14310.1082-0.1286-0.21620.0175-0.0997-0.04450.2218-0.0401-0.01180.2092-0.01460.2166-6.9958-33.7133-18.7764
71.90130.94440.06792.9415-2.01099.3880.0238-0.012-0.0649-0.21470.12160.16150.3866-0.1726-0.15110.1983-0.0305-0.03020.1968-0.01930.274-15.2426-36.3596-32.0756
82.991-1.291-3.5565.1315-0.4195.0622-0.3085-0.2716-0.23070.6940.41450.5673-0.0896-0.1845-0.18260.33430.06580.04230.37540.08840.3063-15.949-18.5338-2.8133
99.7788-2.83052.79156.1154-3.00375.9002-0.1404-0.7672-0.17130.79560.51520.4286-0.3024-0.8076-0.45650.44090.0050.00860.45810.03070.4189-21.2419-15.7917-0.0753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 36 )A-2 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 87 )A37 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 111 )A88 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 174 )A112 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 188 )A175 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 215 )A189 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 239 )A216 - 239
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 9 )B1 - 9
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 9 )I1 - 9

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