Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning

The crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 Å resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3₂12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3₂ decreased R (to 22%) and R_free (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R_free to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme.