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- PDB-9o01: Crystal structure of AfOgg1-D140N mutant bound to 8-OG DNA duplex... -

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Basic information

Entry
Database: PDB / ID: 9o01
TitleCrystal structure of AfOgg1-D140N mutant bound to 8-OG DNA duplex in an intermediate state
Components
  • 8-oxoguanine DNA glycosylase/AP lyase
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*CP*T)-3')
KeywordsHYDROLASE / LYASE/DNA / DNA-glycosylase / AP-lyase / LYASE-DNA complex
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
DNA / DNA (> 10) / 8-oxoguanine DNA glycosylase/AP lyase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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-D140N mutant bound to 8-OG DNA duplex in an intermediate 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
B: DNA (5'-D(P*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*CP*T)-3')
C: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0064
Polymers32,9813
Non-polymers241
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.013, 52.839, 53.459
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23166.939 Da / Num. of mol.: 1 / Mutation: D140N
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: DNA chain DNA (5'-D(P*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*CP*T)-3')


Mass: 4866.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG4000, 100 mM MES, pH 6.5, 5% potassium permanganate (saturated)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.11699 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11699 Å / Relative weight: 1
ReflectionResolution: 1.95→40.52 Å / Num. obs: 20265 / % possible obs: 96.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→1.99 Å / Rmerge(I) obs: 1.87 / Num. unique obs: 1176 / CC1/2: 0.215

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40.52 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 1911 9.87 %
Rwork0.2214 --
obs0.2252 19513 82.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 634 1 63 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.712
X-RAY DIFFRACTIONf_dihedral_angle_d24.877522
X-RAY DIFFRACTIONf_chiral_restr0.042362
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.5831250.5359292X-RAY DIFFRACTION18
1.98-20.496980.4359876X-RAY DIFFRACTION57
2.01-2.040.473810.4329752X-RAY DIFFRACTION49
2.04-2.070.39041190.39931102X-RAY DIFFRACTION72
2.07-2.110.43041240.37911189X-RAY DIFFRACTION78
2.11-2.140.34941490.36271262X-RAY DIFFRACTION83
2.14-2.180.31781340.36591314X-RAY DIFFRACTION84
2.18-2.230.39281710.32311305X-RAY DIFFRACTION87
2.23-2.280.33981260.31631325X-RAY DIFFRACTION86
2.28-2.330.31981530.29421357X-RAY DIFFRACTION88
2.33-2.390.32651610.28781388X-RAY DIFFRACTION89
2.39-2.450.36171450.27291356X-RAY DIFFRACTION89
2.45-2.530.3071420.25131372X-RAY DIFFRACTION89
2.53-2.610.28411590.24091394X-RAY DIFFRACTION90
2.61-2.70.26141460.22931381X-RAY DIFFRACTION90
2.7-2.810.20741560.22661385X-RAY DIFFRACTION91
2.81-2.940.28431660.22421410X-RAY DIFFRACTION91
2.94-3.090.30521540.22631390X-RAY DIFFRACTION91
3.09-3.290.24061590.18561404X-RAY DIFFRACTION92
3.29-3.540.20941550.17791400X-RAY DIFFRACTION91
3.54-3.890.19851550.15651419X-RAY DIFFRACTION92
3.89-4.460.19611550.16151389X-RAY DIFFRACTION91
4.46-5.610.20111490.18781401X-RAY DIFFRACTION92
5.62-40.520.27681400.20761480X-RAY DIFFRACTION94

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