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

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Basic information

Entry
Database: PDB / ID: 7oue
TitleCrystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate
Components
  • DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / archaea / Pyrococcus abyssi
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
: / PHOSPHATE ION / DNA / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 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 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 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 1.3Oct 9, 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')
C: N-glycosylase/DNA lyase
D: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
E: N-glycosylase/DNA lyase
F: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
G: N-glycosylase/DNA lyase
H: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,38211
Polymers122,1538
Non-polymers2293
Water12,989721
1
A: N-glycosylase/DNA lyase
B: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,5382
Polymers30,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-7 kcal/mol
Surface area11520 Å2
MethodPISA
2
C: N-glycosylase/DNA lyase
D: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6333
Polymers30,5382
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area11420 Å2
MethodPISA
3
E: N-glycosylase/DNA lyase
F: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5773
Polymers30,5382
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area11700 Å2
MethodPISA
4
G: N-glycosylase/DNA lyase
H: DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6333
Polymers30,5382
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.743, 74.259, 101.726
Angle α, β, γ (deg.)92.480, 100.740, 105.460
Int Tables number1
Space group name H-MP1

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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.: 4
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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: spermine, MES, PEG 400

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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: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.04→99.46 Å / Num. obs: 68577 / % possible obs: 98.1 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.4
Reflection shellResolution: 2.04→2.08 Å / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3476 / CC1/2: 0.766

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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: 1xqo

1xqo


Resolution: 2.04→71.23 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 3345 4.88 %
Rwork0.1754 65206 -
obs0.1777 68551 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.57 Å2 / Biso mean: 33.418 Å2 / Biso min: 12.01 Å2
Refinement stepCycle: final / Resolution: 2.04→71.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 599 11 721 8963
Biso mean--55.59 36.37 -
Num. residues----1001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.070.33731300.25472748287897
2.07-2.10.3091390.22912683282297
2.1-2.130.26811330.21062680281397
2.13-2.170.2591280.19962713284197
2.17-2.20.25751530.19432719287297
2.2-2.240.24751710.192605277697
2.24-2.290.22551430.18922671281498
2.29-2.330.24751340.17642782291698
2.33-2.390.2391480.17862634278297
2.39-2.440.24671440.17792713285798
2.44-2.50.24291490.17882708285798
2.5-2.570.23951710.17792659283098
2.57-2.640.24961240.19532793291798
2.64-2.730.24911150.19072666278198
2.73-2.830.26381240.18282787291198
2.83-2.940.2521650.18552636280198
2.94-3.070.21271410.19132794293599
3.08-3.240.29221380.18212691282999
3.24-3.440.23661320.18482735286799
3.44-3.710.19931380.17282777291599
3.71-4.080.20881300.15152749287999
4.08-4.670.17671240.13292759288399
4.67-5.880.18031330.16072756288999
5.88-71.230.16071380.1692748288699
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)
10.835-0.4281-0.22411.44110.62672.20280.0195-0.01680.0389-0.06140.0751-0.0877-0.04020.0454-0.08680.1132-0.06040.00440.16340.01180.157917.8493-3.256310.2572
21.6448-0.3041-0.25332.24890.55851.401-0.0165-0.0229-0.1126-0.00340.03450.23220.0633-0.0829-0.01150.1233-0.0595-0.0060.18750.01980.17319.126-9.85928.7166
32.2295-0.88661.6343.0837-0.75513.43420.0457-0.05470.03670.34860.0481-0.07650.09920.0388-0.10170.1694-0.00570.01870.2334-0.01360.151516.5035-4.833328.8398
42.6186-2.7145-3.0785.07411.75124.99840.1782-0.676-0.47220.5805-0.2036-0.3310.54580.4933-0.05180.31470.0077-0.05360.33640.13930.358322.4336-20.405613.423
51.4934-0.08760.10782.30330.22037.4034-0.0448-0.1924-0.10980.16450.02790.14770.0804-0.0830.01980.1826-0.0322-0.00660.1910.03910.23854.220218.171320.8292
61.7647-0.57080.04312.8047-0.84911.1250.02190.04520.0279-0.17630.0519-0.00620.00080.0346-0.06210.1613-0.057-0.00020.16440.00990.16367.587829.01887.7757
72.4013-1.1162-0.61694.8288-0.14783.4889-0.1178-0.0555-0.04090.47740.13760.321-0.0522-0.0861-0.02810.2124-0.00580.03540.24460.01930.16431.764525.309930.5582
82.8764-2.12753.61043.9635-0.82415.96570.2371-1.07160.6210.0348-0.31490.5503-0.2797-0.3691-0.0220.28640.00920.01880.3206-0.09360.4526-1.995341.011913.4025
90.53560.00140.61121.5786-1.94546.20510.13110.1131-0.094-0.2469-0.0365-0.01010.76880.3345-0.12150.31910.0561-0.05670.2278-0.02840.20565.5948-8.2332-38.686
103.09390.61690.35993.52990.83761.30090.1005-0.07010.0010.1144-0.01010.0266-0.0383-0.1136-0.07780.26480.0514-0.02750.1772-0.00240.13792.82393.2564-23.8261
112.4056-0.6301-0.67873.4635-1.6056.62260.07590.33390.2873-0.4007-0.0962-0.4813-0.13180.7445-0.02220.36060.0153-0.03570.4143-0.02240.29694.6892-0.5959-46.5259
126.2105-3.65744.56816.74130.97616.69860.63710.6630.708-0.828-0.6031-0.5416-0.11640.2361-0.05930.5526-0.08910.0670.20630.11990.537410.049416.213-29.484
130.8649-0.0215-0.18952.8379-0.55551.86760.0298-0.0092-0.05080.05470.05970.0288-0.01410.0155-0.1020.21240.0215-0.00260.157-00.207215.756339.4787-27.1755
143.36810.36020.60594.15620.494.0148-0.06360.4162-0.2662-0.83410.01850.3367-0.0301-0.6143-0.02310.4166-0.0044-0.01950.4279-0.00180.275914.127440.7553-46.431
154.6057-2.6553-5.31837.7649-0.09797.75370.1512-0.0294-0.3636-0.6039-0.4028-0.2358-0.30750.02450.23960.3885-0.0875-0.1050.2222-0.0970.475811.929123.6258-29.24
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 87 )A-2 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 159 )A88 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 239 )A160 - 239
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 9 )B1 - 9
5X-RAY DIFFRACTION5chain 'C' and (resid -2 through 36 )C-2 - 36
6X-RAY DIFFRACTION6chain 'C' and (resid 37 through 174 )C37 - 174
7X-RAY DIFFRACTION7chain 'C' and (resid 175 through 239 )C175 - 239
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 9 )D1 - 9
9X-RAY DIFFRACTION9chain 'E' and (resid -2 through 36 )E-2 - 36
10X-RAY DIFFRACTION10chain 'E' and (resid 37 through 159 )E37 - 159
11X-RAY DIFFRACTION11chain 'E' and (resid 160 through 239 )E160 - 239
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 9 )F1 - 9
13X-RAY DIFFRACTION13chain 'G' and (resid -2 through 159 )G-2 - 159
14X-RAY DIFFRACTION14chain 'G' and (resid 160 through 238 )G160 - 238
15X-RAY DIFFRACTION15chain 'H' and (resid 3 through 9 )H3 - 9

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