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The structure of yeast iso-1-cytochrome c has been refined against X-ray
diffraction data to a nominal resolution of 1.23 A. The atomic model contains
893 protein atoms, as well as 116 water molecules and one sulfate anion. Also
included in the refinement are 886 hydrogen atoms belonging to the protein
molecule. The crystallographic R-factor is 0.192 for the 12,513 reflections with
F greater than or equal to 3 sigma (F) in the resolution range 6.0 to 1.23 A.
Co-ordinate accuracy is estimated to be better than 0.18 A. The iso-1-cytochrome
c molecule has the typical cytochrome c fold, with the polypeptide chain
organized into a series of alpha-helices and reverse turns that serve to envelop
the heme prosthetic group in a hydrophobic pocket. Inspection of the
conformations of helices in the molecule shows that the local environments of
the helices, in particular the presence of intrahelical threonine residues,
cause distortions from ideal alpha-helical geometry. Analysis of the internal
mobility of iso-1-cytochrome c, based on refined crystallographic temperature
factors, shows that the most rigid parts of the molecule are those that are
closely associated with the heme group. The degree of saturation of
hydrogen-bonding potential is high, with 90% of all polar atoms found to
participate in hydrogen bonding. The geometry of intramolecular hydrogen bonds
is typical of that observed in other high-resolution protein structures. The 116
water molecules present in the model represent about 41% of those expected to be
present in the asymmetric unit. The majority of the water molecules are
organized into a small number of hydrogen-bonding networks that are anchored to
the protein surface. Comparison of the structure of yeast iso-1-cytochrome c
with those of tuna and rice cytochromes c shows that these three molecules have
very high structural similarity, with the atomic packing in the heme crevice
region being particularly highly conserved. Large conformational differences
that are observed between these cytochromes c can be explained by amino acid
substitutions. Additional subtle differences in the positioning of the
side-chains of several highly conserved residues are also observed and occur due
to unique features in the local environments of each cytochrome c
molecule.(ABSTRACT TRUNCATED AT 400 WORDS)
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