1. Starting structures
To model the AraC/DNA complex we used the structure of the dimerized,
arabinose-bound DD determined by X-ray crystallography (2ARC) and the
structure of the DBD determined by NMR (2K9S). Residues 7-167 are in the
structure of both DDs along with a portion of the linker, residues
168-170. The full linker, residues 168-174 (NESLHPP), is present in the
DD, chain C, with no L-arabinose (1XJA).