User:Eric Martz/Cavities tests: Difference between revisions

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===Structural Alignment with Closest Hit at PDB===

When the [[PDB]] is searched with the dnaC sequence, the closest hit is 39% identity with residues 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 structurally aligned 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="red">Residues 21-63 of 2CHG</font> aligned with <font color="#6060ff">residues 80-124 of the dnaC homology model</font>. (Non-aligned portions are pastel.) This result adds some confidence to 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).

When the [[PDB]] is searched with the dnaC sequence, the closest hit is 39% identity with residues 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 structurally aligned 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. Residues 21-63 of 2CHG aligned with residues 80-124 of the dnaC homology model. This result adds some confidence to 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).

==Crystal Structure of DnaC==

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 ===Structural Alignment with Closest Hit at PDB===
-<applet load='2chg9-63_aligned_with_dnac_model.pdb' size='300' frame='true' align='right' caption='Residues 9-63 structurally aligned with the homology model of dnaC.' />
+<applet load='2chg9-63_aligned_with_dnac_model.pdb' size='400' frame='true' align='right' caption='Residues 9-63 structurally aligned with the homology model of dnaC.' scene='User:Eric_Martz/Sandbox_4/2chg9-63_aligned_with_dnac_mod/1'/>
+When the [[PDB]] is searched with the dnaC sequence, the closest hit is 39% identity with residues 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 structurally aligned 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 &Aring;. <font color="red">Residues 21-63 of 2CHG</font> aligned with <font color="#6060ff">residues 80-124 of the dnaC homology model</font>. (Non-aligned portions are pastel.) This result adds some confidence to 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).
-When the [[PDB]] is searched with the dnaC sequence, the closest hit is 39% identity with residues 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 structurally aligned 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 &Aring;. Residues 21-63 of 2CHG aligned with residues 80-124 of the dnaC homology model. This result adds some confidence to 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).
+{{Clear}}
 ==Crystal Structure of DnaC==