The crystal structure of the hypothetical protein YqgQ from Bacillus subtilis has been determined to 2.1 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 51.85, b = 41.25, c = 55.18 A, beta = 113.4 degrees , and contained three protein molecules in the asymmetric unit. The structure was determined by the single-wavelength anomalous dispersion method using selenium-labeled protein and was refined to a final R factor of 24.7% (R(free) = 28.0%). The protein molecule mainly comprises a three-helical bundle. Its putative function is inferred to be single-stranded nucleic acid binding based on sequence and structural homology.