Structure of E. coli DnaC helicase loader: Difference between revisions
Eric Martz (talk | contribs) →Homology Model Construction: added note explaining "me" |
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The second best sequence-identity hit in the PDB is 39% identity with 54 amino acids (positions 9-63 of chain A) of replication factor C ([[2chg]]), which align with 72-124 of DnaC. When the above homology model of DnaC (made with template 2QGZ) is <scene name='User:Eric_Martz/Sandbox_4/2chg9-63_aligned_with_dnac_mod/1'>structurally aligned</scene> with residues 9-63 of 2CHG<ref>Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.</ref>, 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 Å. <font color="#ff0000">'''Residues 21-63 of 2CHG'''</font> aligned with <font color="#3030ff">'''residues 80-124 of the DnaC homology model'''</font>. (Non-aligned portions are pastel.) This result adds firther confidence to this region of the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in DnaC). | The second best sequence-identity hit in the PDB is 39% identity with 54 amino acids (positions 9-63 of chain A) of replication factor C ([[2chg]]), which align with 72-124 of DnaC. When the above homology model of DnaC (made with template 2QGZ) is <scene name='User:Eric_Martz/Sandbox_4/2chg9-63_aligned_with_dnac_mod/1'>structurally aligned</scene> with residues 9-63 of 2CHG<ref>Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.</ref>, 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 Å. <font color="#ff0000">'''Residues 21-63 of 2CHG'''</font> aligned with <font color="#3030ff">'''residues 80-124 of the DnaC homology model'''</font>. (Non-aligned portions are pastel.) This result adds firther confidence to this region of the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in DnaC). | ||
''Download'' the above structural alignments: | ''Download'' the above structural alignments: | ||
*[[:Image:2qgz_3ec2_aligned.pdb|2qgz_3ec2_aligned.pdb]] | *[[:Image:2qgz_3ec2_aligned.pdb|2qgz_3ec2_aligned.pdb]] | ||
*[[:Image:2chg9-63_aligned_with_dnac_model.pdb|2chg9-63_aligned_with_dnac_model.pdb]] | *[[:Image:2chg9-63_aligned_with_dnac_model.pdb|2chg9-63_aligned_with_dnac_model.pdb]] | ||
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==Crystal Structure of DnaC Is "In The Pipeline"== | ==Crystal Structure of DnaC Is "In The Pipeline"== | ||