Three‐dimensional structure of phenylalanyl‐transfer RNA synthetase from Thermus thermophilus HB8 at 0.6‐nm resolution

The three‐dimensional structure of the heterodimeric α 2 β 2 enzyme phenylalanyl‐tRNA synthetase from Thermus thermophilus HB8 has been determined by X‐ray crystallography, using the multiple‐isomorphous‐replacement method at 0.6 nm resolution. Trigonal crystals of space group P3 2 21 have cell dimensions a = b = 17.6 nm and c = 14.2 nm. Assuming one heterodimeric molecule/asymmetric unit, the ratio of unit cell volume/molecular mass was V = 0.00244 nm 3 /Da, which is in the middle of the range normally observed. However, after a rotation‐function calculation and measurement of the density of the native crystals, we postulate the existence of only the αβ dimer in the asymmetric units. This implies 73% solvent content in the unit cell. Three heavy‐atom derivatives [K 2 PtCl 4 , KAu(CN) 2 and Hg(CH 3 COO) 2 ] and the solvent‐flattening procedure were used for electron‐density‐map calculations. This map confirmed our hypothesis and revealed a remarkably large space filled by solvent, with αβ dimer only in the asymmetric unit. The phenylalanyl‐tRNA synthetase from T. thermophilus molecule has a ‘quasi‐linear’ subunit organization. As can be concluded at this level of resolution, there is no contact between small α subunits in the functional heterodimer.