8DWD | pdb_00008dwd

Adenine glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with an AP site generated by the enzyme acting on purine

• PDB DOI: https://doi.org/10.2210/pdb8DWD/pdb
• NAKB: 8DWD

• Classification: HYDROLASE/DNA
• Organism(s): Geobacillus stearothermophilus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-08-01 Released: 2023-08-09 
• Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY

Russelburg, L.P., Demir, M., Cedeno, K., David, S.S., Horvath, M.P.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 48.85 kDa 
• Atom Count: 3,359 
• Modeled Residue Count: 368 
• Deposited Residue Count: 387 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine DNA glycosylase	A	365	Geobacillus stearothermophilus	Mutation(s): 1  EC: 3.2.2.31
UniProt
Find proteins for P83847 (Geobacillus stearothermophilus) Explore P83847  Go to UniProtKB:  P83847

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')	B	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*CP*AP*(ORP)P*GP*TP*CP*T)-3')	C	11	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	D [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.74	α = 90
b = 85.92	β = 90
c = 140.69	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1905304
National Science Foundation (NSF, United States)	United States	1905249
National Science Foundation (NSF, United States)	United States	1610721
National Science Foundation (NSF, United States)	United States	1608934

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary