7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.

Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D, Nucleic Acids Res (2023) Europe PMC

SASDQ89 – 7-deazapurine in DNA protein B

DGQHR domain-containing protein
MWexperimental 86 kDa
MWexpected 88 kDa
VPorod 126 nm3
log I(s) 1.83×101 1.83×100 1.83×10-1 1.83×10-2
DGQHR domain-containing protein small angle scattering data  s, nm-1
ln I(s)
DGQHR domain-containing protein Guinier plot ln 1.83×101 Rg: 3.4 nm 0 (3.4 nm)-2 s2
(sRg)2I(s)/I(0)
DGQHR domain-containing protein Kratky plot 1.104 0 √3 sRg
Dmax: 13.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DGQHR domain-containing protein ALPHAFOLD model
DGQHR domain-containing protein BILBOMD model
log I(s)
 s, nm-1
DGQHR domain-containing protein ALPHAFOLD model
log I(s)
 s, nm-1
DGQHR domain-containing protein BILBOMD model
Synchrotron SAXS data from solutions of 7-deazapurine in DNA protein B in 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample at 3 mg/ml was injected at a 0.50 ml/min flow rate onto a Shodex PROTEIN KW-802.5 size exclusion column (8.0 mm I.D. x 300 mm) at 24.9°C. Scattering images were collected with 3-s exposures per frame over the course of 40 minutes. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Sample injection volume = UNKNOWN

DGQHR domain-containing protein (DpdB)
Mol. type   Protein
Organism   Salmonella enterica subsp. enterica serovar Montevideo
Olig. state   Dimer
Mon. MW   44.2 kDa
 
UniProt   A0A3Y0E1G8 (1-375)
Sequence   FASTA