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- PDB-7ou3: Crystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase fr... -

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Basic information

Entry
Database: PDB / ID: 7ou3
TitleCrystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase from Thermococcus gammatolerans
ComponentsN-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / archaea / Thermococcus gammatolerans
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
N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesThermococcus gammatolerans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsCoste, F. / Confalonieri, F. / 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

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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)62,2996
Polymers62,0442
Non-polymers2554
Water5,747319
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0572
Polymers31,0221
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2414
Polymers31,0221
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.429, 62.452, 139.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 31021.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: TGAM_1653 / Production host: Escherichia coli (E. coli)
References: UniProt: C5A7E3, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Hepes, NaCl, PEG 1500, glycerol

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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 EIGER2 X 16M / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.49→69.94 Å / Num. obs: 88713 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.6
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4393 / CC1/2: 0.832 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xqo

1xqo


Resolution: 1.49→46.15 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1918 4390 4.95 %
Rwork0.1722 84309 -
obs0.1732 88699 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 14 319 4185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554011
X-RAY DIFFRACTIONf_angle_d0.7665457
X-RAY DIFFRACTIONf_chiral_restr0.0698607
X-RAY DIFFRACTIONf_plane_restr0.0073705
X-RAY DIFFRACTIONf_dihedral_angle_d11.61821487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.25771350.23512753X-RAY DIFFRACTION99.97
1.51-1.520.23841430.22322782X-RAY DIFFRACTION99.9
1.52-1.540.26681320.21072805X-RAY DIFFRACTION100
1.54-1.560.21481420.20912773X-RAY DIFFRACTION99.9
1.56-1.580.23521760.20242747X-RAY DIFFRACTION99.97
1.58-1.60.22951370.19552772X-RAY DIFFRACTION100
1.6-1.630.20871330.21272803X-RAY DIFFRACTION100
1.63-1.650.21171300.20762796X-RAY DIFFRACTION99.97
1.65-1.680.22981580.20752780X-RAY DIFFRACTION100
1.68-1.70.22471440.20242779X-RAY DIFFRACTION99.97
1.7-1.730.24011460.18772776X-RAY DIFFRACTION99.97
1.73-1.770.19271430.17222792X-RAY DIFFRACTION99.93
1.77-1.80.1851680.17382768X-RAY DIFFRACTION99.97
1.8-1.840.17851630.1692775X-RAY DIFFRACTION100
1.84-1.880.20351470.16872776X-RAY DIFFRACTION99.93
1.88-1.920.22811340.16982832X-RAY DIFFRACTION99.97
1.92-1.970.19461380.17762790X-RAY DIFFRACTION100
1.97-2.020.20581540.19062785X-RAY DIFFRACTION100
2.02-2.080.16831510.1652802X-RAY DIFFRACTION99.97
2.08-2.150.19561500.17082793X-RAY DIFFRACTION100
2.15-2.220.19811390.16622820X-RAY DIFFRACTION99.9
2.22-2.310.18351220.16722852X-RAY DIFFRACTION100
2.31-2.420.1871360.16572818X-RAY DIFFRACTION99.86
2.42-2.550.20321700.16772791X-RAY DIFFRACTION100
2.55-2.710.17721580.16822836X-RAY DIFFRACTION100
2.71-2.910.18381410.16532841X-RAY DIFFRACTION99.97
2.92-3.210.17381660.16912827X-RAY DIFFRACTION99.97
3.21-3.670.15091450.16292902X-RAY DIFFRACTION99.87
3.67-4.630.17721390.14772900X-RAY DIFFRACTION99.87
4.63-46.150.22371500.18643043X-RAY DIFFRACTION99.5
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)
13.39148127705-2.57989724339-2.320127196472.853322015071.591082912691.85215964019-0.175888602456-0.310680405975-0.3170548793970.1369453115310.108295261266-0.08953517026840.2573658072270.326329732830.06134641974890.1988473249240.0442048030733-0.006054829532920.2233777764780.01418108064410.26067402914294.3791562321180.044834276281.987859503
21.436439929090.457719220298-0.3544963064721.9921581137-0.09153492873081.978237875630.0696747471130.01457593417380.031272523106-0.0183850553127-0.03459554814060.0540932553403-0.117192043196-0.0531796861349-0.03680956082910.1225760878050.008993621848150.01843756573170.1578898128160.001208981349250.14738155237381.2148935857196.797885955279.115068678
35.99949151243-2.33659936368-2.472433690813.78271004581.792424344431.995901447550.257162533826-0.1374400117510.310068321584-0.405271404635-0.020975773534-0.772632082493-0.1970661142010.336719383603-0.2114932710970.2859381071080.02473101321690.06720414160220.2202370031720.01207185170350.37873284332397.7847161091180.076081711275.898951641
41.312169419741.245765732620.4516438721462.709074525240.1722696152754.03667313977-0.378705055726-0.09744996037910.05702949073750.0204883403168-0.0209348624151-0.628598914297-0.4799858128140.575519658350.2748386109010.273156099511-0.0951718267555-0.03212899473630.2933579043210.07217665441120.2776473954279.0507644294189.392812959325.138213558
50.800935715117-0.0292424540409-0.06022668174632.29156755191-0.2511145122051.6696990847-0.02722210190820.0143131778379-0.02295971330010.01774572506720.02590923760130.08915482646910.049400750477-0.0621735913576-0.0002326710552120.117369750873-0.001746440856970.001196053207760.121715736698-0.0004961503471430.12093895166460.5582009513195.04251805305.268368778
62.484018740210.1315629891021.075615518833.02474765772-0.4783641146361.76713650017-0.4569374587740.3619636950170.188109883944-0.4184105811480.205439035154-0.896839450852-0.7921960980860.8208169175820.1321363467940.449643733384-0.2238213137660.04336683221960.4083502022470.03605357243560.38509750872479.170630808189.884676663317.451617202
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 54 )AA11 - 541 - 44
22chain 'A' and (resid 55 through 180 )AA55 - 18045 - 170
33chain 'A' and (resid 181 through 263 )AA181 - 263171 - 248
44chain 'B' and (resid 14 through 39 )BB14 - 391 - 26
55chain 'B' and (resid 40 through 180 )BB40 - 18027 - 167
66chain 'B' and (resid 181 through 263 )BB181 - 263168 - 241

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