X-ray analysis of a [2Fe-2S] ferrodoxin from Spirulina platensis. Main chain fold and location of side chains at 2.5 A resolution.

Abstract

A [2Fe-2S] ferrodoxin from Spirulina platensis crystallized in space group C2221 with cell dimensions of a = 62.32, b = 28.51, c = 108.08 A, and alpha = beta = gamma = 90.0 degrees. X-ray structure analysis of the protein was carried out at 2.5 A resolution by the single isomorphous replacement method coupled with the derivative and the native anomalous dispersion methods. Phase angles of 2182 independent reflections were determined and their average figure of merit was 0.58. Each of 98 residues was superposed on the electron density sections enlarged to 2 cm/l A with a half-mirror device (Richards box). About 25% of the total residues form beta-structure and 10% fold in a tow-turn alpha-helix. A beta-barrel-like structure was found in the main chain fold. A polypeptide segment from residues 41 to 49 forms a loop structure outside the barrel. Two iron atoms of the [2Fe-2S] cluster are coordinated by three cysteines in the loop and by Cys-79. Hydrogen bonds of NH....S and OH....S stabilize the loop conformation. Most side chains are reasonably oriented in the molecule. The internal volume of the barrel is occupied by aliphatic nonpolar residues. All the charged groups are accessible to solvent molecules.