4 - Central Institute of Brackishwater Aquaculture

Natlonal Workshop-cum-~ralnlng on EUoinformatics and Information Management in Aquaculturn
The comparison in Figure 4 shows that 1hqc:A and lin4:A are almost identical,
both sequentially and structurally. However, lin4:A has a better crystallographic
resolution (3.28, versus 1.68)~ eliminating lhqc:A[yamada et al., 19971. A
second group of structures (liqp:A, 1sxj:c) share some similarities. From this
group, lsxj [Bowman et al., 19971 has the poorest resolution leaving for
consideration only 1iqp:A. 3cf2:A [Davies et al., 19971 is the most diverse
structure of the whole set of possible templates. However, it is the one with the
lowest sequence identity (26%) to the query sequence. Finally taken lin4:A over
instead of liqp:A[Oyama et al., 19971 because of its better resolution versus
1.68, , its better crystallographic R-factor (23.4O10) and higher overall sequence
identity to the query sequence (53%). The protein was modelled with best
template lin4. The flnal structure of modelled protein is shown in Figure 5.
Figure 5: Predicted 3-D structure of Holliday junction DNA helicase RuvB protein.
The modeled protein is validated with the SAVES server. The results of the
PROCHECK analysis indicate that a relatively low percentage of residues have
phi/psi angles in the disallowed ranges, the quality of Ramchandran plots is
acceptable [Ramachandran et al., 19631. The percentage of residues in the
"core" region of modeled was found to be 94.2%. The stereochemical quality of
the model was found to be satisfactory. The Ramachandran plot of the modeled
protein is shown in Figure 6.