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Figure 4.8: MurA (open form)
Morph ID: f805267-29412 PDB ID: 1EJD
HAG hinges: 20,21,228,229
This protein is composed of a continuous domain (residues 21-228, in green above) and a
discontinuous domain (residues 1-20 and 229-419, in pink and blue, respectively). There
is a clear region of high FlexOracle energy and another of intermediate energy, with the
boundary arguably at residue 232. The N-terminal boundary of the continuous domain is
less clear.
As in the case of Glutamine Binding Protein, StoneHinge did not predict the second
largest domain as a single domain, instead predicting it as multiple smaller domains.
Again, the StoneHinge output noted that its prediction did not correspond to domain
motion.
TLSMD finds the domain boundary at 228/229 in all partitions (N=2,3,4,5), but does not
find the boundary at 20/21 until N=6. TLSMD analyses of the two peptide chains in
1EJD are consistent in this regard (8.c). TLSMD 6-group boundaries for 1EJD chains A
and B. The continuous domain consisting of residues 21-228 is broken into 3 segments
(green/magenta/red) by TLSMD, which may be interpreted as due to local flexibility of
the loop of residues (108-127) at the top of the green domain in Figure 4.8a.
230