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

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Basic information

Entry
Database: PDB / ID: 7olb
TitleCrystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi
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
CITRIC ACID / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,69112
Polymers27,9831
Non-polymers70811
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.570, 35.920, 46.490
Angle α, β, γ (deg.)95.504, 91.889, 108.410
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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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Non-polymers , 5 types, 207 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: LiCl, tri-Na citrate, PEG6000

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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: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.1→46.17 Å / Num. obs: 84275 / % possible obs: 95.7 % / Redundancy: 7 % / Biso Wilson estimate: 11.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.5
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4021 / CC1/2: 0.954

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xg7

1xg7


Resolution: 1.1→46.17 Å / SU ML: 0.0902 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.0718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1572 4031 4.78 %
Rwork0.1437 80238 -
obs0.1444 84269 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.65 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 44 196 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782102
X-RAY DIFFRACTIONf_angle_d1.0072853
X-RAY DIFFRACTIONf_chiral_restr0.0755314
X-RAY DIFFRACTIONf_plane_restr0.0068360
X-RAY DIFFRACTIONf_dihedral_angle_d26.2777809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.22261390.19352679X-RAY DIFFRACTION92.18
1.11-1.130.21581100.16982631X-RAY DIFFRACTION91.89
1.13-1.140.19291100.15572732X-RAY DIFFRACTION93.24
1.14-1.160.18251330.15122717X-RAY DIFFRACTION92.5
1.16-1.170.17021350.13812657X-RAY DIFFRACTION93.69
1.17-1.190.14131350.13552740X-RAY DIFFRACTION93.44
1.19-1.210.13741390.13192678X-RAY DIFFRACTION93.43
1.21-1.220.1411420.13132732X-RAY DIFFRACTION94.23
1.22-1.250.15451570.13072672X-RAY DIFFRACTION93.8
1.25-1.270.15221260.12882797X-RAY DIFFRACTION94.78
1.27-1.290.14311300.13022687X-RAY DIFFRACTION94.15
1.29-1.310.15081340.12452781X-RAY DIFFRACTION95.01
1.31-1.340.14371550.13022712X-RAY DIFFRACTION95
1.34-1.370.15171620.12992761X-RAY DIFFRACTION95.49
1.37-1.40.15251290.1312754X-RAY DIFFRACTION95.59
1.4-1.440.15691310.12962808X-RAY DIFFRACTION95.73
1.44-1.480.14481350.12872735X-RAY DIFFRACTION96.28
1.48-1.520.14291240.12222807X-RAY DIFFRACTION96.35
1.52-1.570.13851440.12322793X-RAY DIFFRACTION96.55
1.57-1.620.15991310.12972826X-RAY DIFFRACTION96.92
1.62-1.690.14171300.12972858X-RAY DIFFRACTION97.3
1.69-1.770.16131300.13712776X-RAY DIFFRACTION97.58
1.77-1.860.16191290.13852885X-RAY DIFFRACTION97.73
1.86-1.980.13651710.13492787X-RAY DIFFRACTION97.95
1.98-2.130.1461470.13192838X-RAY DIFFRACTION98.55
2.13-2.340.12491650.13852837X-RAY DIFFRACTION98.62
2.34-2.680.15761580.14082834X-RAY DIFFRACTION98.97
2.68-3.380.161530.15432871X-RAY DIFFRACTION99.51
3.38-46.170.19351470.17192853X-RAY DIFFRACTION98.46

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