Pseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase

Two trigonal crystal structures of naphthalene 1,2-dioxygenase from Pseudomonas sp. NCIB 9816-4 have been refined at 2.6 Å resolution. The space group is R3, with four heterodimers in the asymmetric unit. The crystallographic threefold axis coincides with the symmetry axis of the active molecule, a mushroom-shaped α₃β₃ hexamer. The crystal is formed by symmetrical contacts between the hexamers on three different interaction surfaces, one on the β-subunit and the other two on the α-­subunits. Nickel ions mediate one of the α-subunit interactions. The two other types of packing contacts sustain two interlaced and almost independent crystal patterns with significantly different temperature factors. The space group of the individual crystal patterns is R32, with the corresponding twofold axes parallel to each other. The interactions between the crystal patterns separate the two parallel twofolds, eliminating the twofold symmetry for the whole crystal. The differences in temperature factors among the molecules in the asymmetric unit have been refined and are different for the two refined structures. An analysis of the structure factors of the pseudo-equivalent reflections showed that their differences lie in their phases and not in their amplitudes, suggesting that R_merge is not an appropriate indicator for revealing the correct point group.