Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7

Marusa Prolic Kalinsek.

SASDV54 – YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA.

Phage antirepressor protein Cro
IR1 22 base pair dsDNA
MWexperimental 35 kDa
MWexpected 37 kDa
VPorod 53 nm3
log I(s) 1.40×102 1.40×101 1.40×100 1.40×10-1
Phage antirepressor protein Cro IR1 22 base pair dsDNA small angle scattering data  s, nm-1
ln I(s)
Phage antirepressor protein Cro IR1 22 base pair dsDNA Guinier plot ln 1.40×102 Rg: 2.8 nm 0 (2.8 nm)-2 s2
(sRg)2I(s)/I(0)
Phage antirepressor protein Cro IR1 22 base pair dsDNA Kratky plot 1.104 0 3 sRg
p(r)
Phage antirepressor protein Cro IR1 22 base pair dsDNA pair distance distribution function Rg: 2.9 nm 0 Dmax: 10.1 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Phage antirepressor protein Cro IR1 22 base pair dsDNA OTHER [STATIC IMAGE] model

Synchrotron SAXS data from solutions of YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA in 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH 5.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.0992 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 45.00 μl sample at 15 mg/ml was injected at a 0.16 ml/min flow rate onto a Agilent AdvanceBio SEC 300Å, 4.6 x 150 mm column at 15°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The atomic coordinates of the full model ensemble are made available in the full entry zip archive. X-ray exposure time = UNKNOWN. Number of sample data frames = UNKNOWN.

Phage antirepressor protein Cro (YdaS protein)
Mol. type   Protein
Organism   Escherichia coli O157:H7
Olig. state   Dimer
Mon. MW   11.9 kDa
 
UniProt   Q8XAD7 (1-100)
Sequence   FASTA
 
IR1 22 base pair dsDNA (IR1)
Mol. type   DNA
Olig. state   Monomer
Mon. MW   13.6 kDa
Sequence   FASTA