9O03 | pdb_00009o03

Crystal structure of AfOgg1:8OG-DNA duplex in a product-bound state

• PDB DOI: https://doi.org/10.2210/pdb9O03/pdb

• Classification: HYDROLASE, LYASE/DNA
• Organism(s): Archaeoglobus fulgidus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-01 Released: 2026-04-15 
• Deposition Author(s): Arvai, A.S., Syed, A., Huffman, J.L., Mol, C.D., Hitomi, K., Tainer, J.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AfOgg1:8OG-DNA duplex in a product-bound state

Arvai, A.S., Syed, A., Huffman, J.L., Mol, C.D., Hitomi, K., Tainer, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.96 kDa 
• Atom Count: 2,273 
• Modeled Residue Count: 228 
• Deposited Residue Count: 231 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-oxoguanine DNA glycosylase/AP lyase	A	203	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: ogg, AF_0371 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for O29876 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29876  Go to UniProtKB:  O29876

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*TP*CP(PUA))-3')	B [auth D]	6	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*CP*TP*GP*CP*A)-3')	C [auth B]	7	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-3')	D [auth C]	15	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.253 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.813	α = 90
b = 44.815	β = 104.29
c = 59.026	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Arvai, A.S., Syed, A., Huffman, J.L., Mol, C.D., Hitomi, K., Tainer, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA220430

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release