Extension of Fe MAD phases in the structure determination of a multiple [FeS] cluster containing hydrogenase

The structure of the hydrogenase (CpI) from Clostridium pasteurianum has been solved by MAD phasing taking advantage of the presence of 20 Fe atoms in the native ~60 kD protein. The Fe atoms in this protein are distributed into five [FeS] clusters that could easily be identified in Patterson maps. Although the individual sites for the Fe atoms within the [FeS] cluster could not be identified directly, phasing to the maximum resolution (2.5 Å) of the MAD data was achieved by an iterative assignment and refinement of the positions of individual Fe atoms based mainly on the known structure of several of the metal clusters. After the majority of the Fe atoms had been successfully assigned and refined in this manner, excellent quality electron-density maps were obtained which allowed the amino acid chain to be traced.