Structure of E. coli DnaC helicase loader: Difference between revisions
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==Confirmation of Homology Model By Related Structures== | ==Confirmation of Homology Model By Related Structures== | ||
When the [[PDB]] is searched with the DnaC sequence, the best match (December, 2008) is 23% sequence identity with 183 amino acids in the DnaC helicase loader of ''Aquifex aeolicus'', [[3ec2]] and [[3ecc]]. In order to find whether these structures have the same fold as the template ([[2qgz]] with 19% sequence identity to ''E. coli'' DnaC) used for the homology model, <font color="#3030ff">'''2qgz'''</font> <scene name='User:Eric_Martz/Sandbox_6/2qgz_3ec2_aligned_pdb/1'>was structurally aligned</scene> with <font color="#ff0000">'''3ec2'''</font><ref>The structural alignment of 2qgz with 3ec2 was performed with the ''Magic Fit'' function of DeepView version 3.6beta2. 2qgz 115-259 aligned with 3ec2 42-185 (3 gaps in 3ec2's alignment: 128-9, 134-5, 155-9). 135 alpha carbons were aligned with RMS 2.76 Å. The sequence identity between 2qgz and 3ec2 is 28% over the 185 amino acid length of the shorter, 3ec2. ''Magic Fit'' is a sequence-alignment-guided structural alignment (see [[Structural_alignment_tools#DeepView_.3D_Swiss-PDBViewer|Structural alignment tools]]).</ref>. The similarity of folds lends considerable confidence to the homology model of ''E. coli'' DnaC. This was further confirmed by the 2012 Swiss Model run, when 3ecc was selected as the best template (see discussion above). | When the [[PDB]] is searched with the DnaC sequence, the best match (December, 2008) is 23% sequence identity with 183 amino acids in the DnaC helicase loader of ''Aquifex aeolicus'', [[3ec2]] and [[3ecc]]. In order to find whether these structures have the same fold as the template ([[2qgz]] with 19% sequence identity to ''E. coli'' DnaC) used for the homology model, <font color="#3030ff">'''2qgz'''</font> <scene name='User:Eric_Martz/Sandbox_6/2qgz_3ec2_aligned_pdb/1'>was structurally aligned</scene> with <font color="#ff0000">'''3ec2'''</font><ref>The structural alignment of 2qgz with 3ec2 was performed with the ''Magic Fit'' function of DeepView version 3.6beta2. 2qgz 115-259 aligned with 3ec2 42-185 (3 gaps in 3ec2's alignment: 128-9, 134-5, 155-9). 135 alpha carbons were aligned with RMS 2.76 Å. The sequence identity between 2qgz and 3ec2 is 28% over the 185 amino acid length of the shorter, 3ec2. ''Magic Fit'' is a sequence-alignment-guided structural alignment (see [[Structural_alignment_tools#DeepView_.3D_Swiss-PDBViewer|Structural alignment tools]]).</ref>. The similarity of folds lends considerable confidence to the homology model of ''E. coli'' DnaC. This was further confirmed by the 2012 Swiss Model run, when 3ecc was selected as the best template (see discussion above). | ||