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- PDB-7oli: Crystal structure of Pab-AGOG in complex with 8-oxoguanosine -

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Basic information

Entry
Database: PDB / ID: 7oli
TitleCrystal structure of Pab-AGOG in complex with 8-oxoguanosine
ComponentsN-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
2'-DEOXY-8-OXOGUANOSINE / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 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: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8429
Polymers55,9652
Non-polymers8777
Water6,053336
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3283
Polymers27,9831
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5146
Polymers27,9831
Non-polymers5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.063, 47.202, 91.271
Angle α, β, γ (deg.)90.000, 100.800, 90.000
Int Tables number5
Space group name H-MC121

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
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: Chemical ChemComp-8HG / 2'-DEOXY-8-OXOGUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: LiCl, tri-Na citrate, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→48.19 Å / Num. obs: 65858 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.3
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9640 / CC1/2: 0.837

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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: 7OLB

7olb


Resolution: 1.65→44.83 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 3279 4.99 %
Rwork0.1614 62444 -
obs0.1628 65723 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.11 Å2 / Biso mean: 31.9071 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 1.65→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 60 336 4249
Biso mean--26.66 40.39 -
Num. residues----484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.26141460.2132700284699
1.67-1.70.25791500.19812727287799
1.7-1.730.23851460.18962675282199
1.73-1.760.20171450.18722676282199
1.76-1.790.24111480.18392730287899
1.79-1.820.21771500.183427332883100
1.82-1.860.23141490.183226522801100
1.86-1.90.22741310.179927662897100
1.9-1.950.23431350.172326752810100
1.95-20.20931510.165327242875100
2-2.050.19611300.16942747287799
2.05-2.110.22111470.16752672281999
2.11-2.180.1891390.1672726286599
2.18-2.260.20721520.16732678283099
2.26-2.350.20421470.1642683283099
2.35-2.450.19231210.16892721284299
2.45-2.580.2061360.16252740287699
2.58-2.740.20531370.16542691282898
2.74-2.960.19241490.16912718286798
2.96-3.250.18931440.16622679282398
3.25-3.720.18711260.15972734286098
3.72-4.690.15271550.13682749290499
4.69-44.830.15891450.14582848299399
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)
17.43733.32671.01955.59442.51555.81890.09860.15-0.6141-0.50780.13560.36830.848-0.2576-0.22430.39320.0186-0.14160.229-0.00810.3451-23.80299.42715.9734
23.7766-0.44990.99714.5887-0.03424.6231-0.05460.10930.28440.01010.1074-0.2746-0.16530.1698-0.05690.13770.01120.0170.1366-0.00680.176-17.038130.444414.2923
35.1412-1.1979-0.84486.39981.16336.5415-0.2437-0.60180.82320.68090.0738-0.4873-0.99460.2470.0290.4030.0104-0.08570.2482-0.09180.403-16.331240.681821.7889
42.9957-1.25560.92853.45550.09533.6822-0.0387-0.45720.27010.35180.26610.2131-0.2541-0.2976-0.14170.33250.06830.04520.2639-0.06270.231-25.715436.118923.404
53.9353-0.2692-2.14723.39961.22561.7159-0.0012-0.3695-0.25730.6470.12630.0553-0.0332-0.3315-0.0830.29230.06180.02730.42450.08720.1538-21.914820.001728.6378
64.18270.04581.53564.1344-0.0943.31470.0566-0.2643-0.34130.13810.18070.22220.1073-0.2235-0.22130.15150.0089-0.01420.19120.03920.1519-21.890218.375318.4893
77.80973.47861.33521.94261.29251.55940.39860.2071-0.3073-0.16040.47210.84980.306-0.5649-0.24310.2585-0.0529-0.22120.4180.18990.599-39.03518.55727.1821
85.24172.23681.61556.8143-0.61062.11230.3163-0.282-0.6176-0.01950.21180.5220.4534-0.3558-0.4770.2265-0.018-0.10350.24650.05790.3365-30.102713.38411.2475
98.3673-0.3184-0.08118.1470.17423.35670.15580.8582-0.5612-0.39610.20890.22810.7742-0.1861-0.37650.5401-0.0289-0.05430.3506-0.05820.2393-23.784513.2277-3.1152
101.51270.29110.36645.06580.37621.72930.0278-0.08150.19330.3934-0.0795-0.13-0.09280.08590.01970.19550.0051-0.03990.147-0.00450.168821.006424.29936.5341
113.8914-0.43390.31873.0704-0.01863.37890.1090.053-0.2265-0.0951-0.03840.19230.3199-0.1261-0.03040.1837-0.0081-0.04130.1323-0.0040.16239.402710.457128.152
126.8503-0.05930.63592.0530.18931.46970.09380.2969-0.1109-0.142-0.07940.1508-0.0364-0.4818-0.02970.16970.0326-0.050.1364-0.00730.17473.24814.135122.139
131.60460.4380.7021.52950.53812.252-0.13360.13450.4921-0.1381-0.1090.0876-0.3717-0.05410.1040.21120.0218-0.0440.14840.03020.249314.702728.976426.8115
146.572.7682.41034.8211.58895.21980.059-0.45150.18240.3519-0.16140.03780.1006-0.45450.0830.3072-0.0231-0.02140.2598-0.01690.232920.477231.027247.7764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 20 )A-2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 69 )A21 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 87 )A70 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 111 )A88 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 141 )A112 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 174 )A142 - 174
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 188 )A175 - 188
8X-RAY DIFFRACTION8chain 'A' and (resid 189 through 215 )A189 - 215
9X-RAY DIFFRACTION9chain 'A' and (resid 216 through 239 )A216 - 239
10X-RAY DIFFRACTION10chain 'B' and (resid -2 through 36 )B-2 - 36
11X-RAY DIFFRACTION11chain 'B' and (resid 37 through 87 )B37 - 87
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 111 )B88 - 111
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 215 )B112 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 239 )B216 - 239

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