In the Gram-positive bacterium Bacillus subtilis the concentration of the amino acid L-arginine is controlled by the transcriptional regulator AhrC. The hexameric AhrC protein binds in an L-arginine-dependent manner to pseudo-palindromic operators within the promoter regions of arginine biosynthetic and catabolic gene clusters. AhrC binding results in the repression of transcription of biosynthetic genes and in the activation of transcription of catabolic genes. The crystal structure of AhrC has been determined at 2.7 A resolution. Each subunit of the protein has two domains. The C-terminal domains are arranged with 32 point-group symmetry and mediate the major intersubunit interactions. The N-terminal domains are located around this core, where they lie in weakly associated pairs but do not obey strict symmetry. A structural comparison of AhrC with the arginine repressor from the thermophile B. stearothermophilus reveals close similarity in regions implicated in L-arginine binding and DNA recognition, but also reveals some striking sequence differences, especially within the C-terminal oligomerization domain, which may contribute to the different thermostabilities of the proteins. Comparison of the crystal structure of AhrC with a 30 A resolution model obtained by combining X-ray structure-factor amplitudes with phases derived from electron-microscopic analyses of AhrC crystals confirms the essential accuracy of the earlier model and suggests that such an approach may be more widely useful for obtaining low-resolution phase information.