X-ray structure determination of a dimeric hemoglobin from Caudina arenicola

The X-ray structure of a dimeric, cyanomet-liganded hemoglobin D-chain (Hb-D) from Caudina arenicola has been determined by the molecular-replacement method. The search model was a concatenated model of three hemoglobin structures superimposed on the backbone of monomeric, hemichrome hemoglobin C-chain (Hb-C) from the same organism. Hb-D crystallizes in space group P4₁2₁2 with cell constants a = b = 77.0 and c =61.5 Å with one subunit in the asymmetric unit. The dimer twofold axis corresponds to a crystallographic twofold along one of the body diagonals of the unit cell. Rotation and translation searches as well as model refinement were carried out in X-PLOR with the final model having an R value of 0.19 using the data from 5.0 to 2.9 Å resolution (R = 0.26 for 10.0 to 2.9 Å resolution). The homodimeric structure of Caudina Hb-D features close heme-heme contacts with an Fe-Fe distance of 19.0 Å. The subunit-subunit interface involves both the E and F helices from each subunit with the E helices oriented antiparallel at 50° with respect to one another, similar to the quaternary structure observed for the homodimeric hemoglobin from Scapharca inaequivalvis.