The crystal structure of myoglobin, V. A low-resolution three-dimensional Fourier synthesis of sperm-whale myoglobin crystals

Abstract

The study of type A crystals of sperm-whale has now been extended to three dimensions by using the method of isomorphous replacement to determine the phases of all the general X-ray reflexions having d > 6 Å, and a three-dimensional Fourier synthesis of the electron density in the unit cell has been computed. Data were obtained from the same derivatives which had been used in the previous two-dimensional study (Bluhm, Bodo, Dintzis & Kendrew 1958), in the course of which the x and z co-ordinates of the heavy atoms had been determined. Several methods were used to determine the y co-ordinates from the three-dimensional data; with a knowledge of all three co-ordinates of each heavy atom it was possible to establish the phases of nearly all the reflexions by a graphical method. The three-dimensional Fourier synthesis was evaluated on a high-speed computer from these phases and from the observed amplitudes of the reflexions. A resolution of 6 Å was chosen because it should clearly reveal polypeptide chains having a compact configuration such as a helix. The electron-density map was in fact found to contain a large number of dense rod-like features which are considered to be polypeptide chains, probably helically coiled. In addition, a very dense flattened disk is believed to be the haem group with its central iron atom. Finally it was possible to identify the boundaries of the protein molecules by locating the intermolecular regions containing salt solution. An isolated myoglobin molecule has dimensions about 45 x 35 x 25 Å and within it the polypeptide chain is folded in a complex and irregular manner. For the most part the course of the chain can be followed, but there are some doubtful stretches, presumably where the helical configuration breaks down; a crude measurement of the total visible length of chain suggests that about 70% of it may be in a helical or some similarly compact configuration. The haem group is near the surface of the molecule.