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- PDB-9o00: Crystal structure of AfOgg1 in a DNA-free state -

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Basic information

Entry
Database: PDB / ID: 9o00
TitleCrystal structure of AfOgg1 in a DNA-free state
Components8-oxoguanine DNA glycosylase/AP lyase
KeywordsHYDROLASE / LYASE / DNA-glycosylase / AP-lyase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / 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
8-oxoguanine DNA glycosylase/AP lyase Ogg / 8-oxoguanine DNA glycosylase / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
8-oxoguanine DNA glycosylase/AP lyase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsHuffman, J.L. / Tang, H.Y.H. / Syed, A. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
CitationJournal: To Be Published
Title: Crystal structure of AfOgg1 in a DNA-free state
Authors: Huffman, J.L. / Tang, H.Y.H. / Syed, A. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
History
DepositionApr 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-oxoguanine DNA glycosylase/AP lyase


Theoretical massNumber of molelcules
Total (without water)23,4021
Polymers23,4021
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10390 Å2
Unit cell
Length a, b, c (Å)86.508, 106.499, 141.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21A-257-

HOH

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Components

#1: Protein 8-oxoguanine DNA glycosylase/AP lyase


Mass: 23402.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: ogg, AF_0371 / Production host: Escherichia coli (E. coli)
References: UniProt: O29876, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM imidazole/malate, pH 5.0, 75% ammonium sulfate (saturated)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→42.57 Å / Num. obs: 21581 / % possible obs: 87.7 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.3
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 1.374 / Num. unique obs: 906

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
AutoSolphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.93→42.57 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2426 1999 9.23 %
Rwork0.2152 --
obs0.2178 21565 86.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 63 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.235
X-RAY DIFFRACTIONf_dihedral_angle_d6.11226
X-RAY DIFFRACTIONf_chiral_restr0.049244
X-RAY DIFFRACTIONf_plane_restr0.012282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.4407730.4832730X-RAY DIFFRACTION46
1.96-1.980.5708920.4416886X-RAY DIFFRACTION55
1.98-2.010.3457950.3699951X-RAY DIFFRACTION60
2.01-2.040.34341000.3587993X-RAY DIFFRACTION63
2.04-2.070.39661100.35061079X-RAY DIFFRACTION66
2.07-2.10.34651140.33791104X-RAY DIFFRACTION70
2.1-2.130.36261250.30981212X-RAY DIFFRACTION77
2.13-2.170.28591280.29061256X-RAY DIFFRACTION78
2.17-2.210.3281430.28141429X-RAY DIFFRACTION89
2.21-2.250.28141510.26561480X-RAY DIFFRACTION95
2.25-2.30.26331630.26081567X-RAY DIFFRACTION98
2.3-2.350.29671580.25561554X-RAY DIFFRACTION98
2.35-2.40.30921620.24881562X-RAY DIFFRACTION98
2.4-2.460.22691610.23691595X-RAY DIFFRACTION98
2.46-2.530.271650.23491578X-RAY DIFFRACTION98
2.53-2.60.27281530.24391513X-RAY DIFFRACTION97
2.6-2.690.25721590.22921576X-RAY DIFFRACTION98
2.69-2.780.22861560.22691537X-RAY DIFFRACTION97
2.79-2.90.25351590.25241550X-RAY DIFFRACTION97
2.9-3.030.28571570.23641553X-RAY DIFFRACTION97
3.03-3.190.27721540.22891550X-RAY DIFFRACTION96
3.19-3.390.23451550.21061533X-RAY DIFFRACTION97
3.39-3.650.18211620.19341542X-RAY DIFFRACTION96
3.65-4.020.20281530.16751519X-RAY DIFFRACTION95
4.02-4.590.18591460.15731519X-RAY DIFFRACTION94
4.6-5.790.20961520.18291484X-RAY DIFFRACTION93
5.8-42.570.22541480.18371474X-RAY DIFFRACTION91

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