Structure of E. coli DnaC helicase loader: Difference between revisions
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This sequence (245 amino acids) was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me<ref>Not clear to [[User:Eric Martz]] in December, 2008.</ref>. The homology model represents residues 55-237 (183 residues representing 75% of DnaC), shown in '''boldface in the above sequence'''. Because of the low sequence identity, this model may well contain significant errors, especially in registration<ref>''Registration'' refers to the positioning of amino acids along the backbone of the homology model. Amino acids are "in register" when correctly positioned. The sequence of the target protein (DnaC) can be thought of as sliding along the template backbone, as a consequence of the process of sequence alignment (or threading). The correct registration will be known only when an empirical crystallographic structure becomes available for DnaC.</ref>. | This sequence (245 amino acids) was submitted to Swiss Model in 2008, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me<ref>Not clear to [[User:Eric Martz]] in December, 2008.</ref>. The homology model represents residues 55-237 (183 residues representing 75% of DnaC), shown in '''boldface in the above sequence'''. Because of the low sequence identity, this model may well contain significant errors, especially in registration<ref>''Registration'' refers to the positioning of amino acids along the backbone of the homology model. Amino acids are "in register" when correctly positioned. The sequence of the target protein (DnaC) can be thought of as sliding along the template backbone, as a consequence of the process of sequence alignment (or threading). The correct registration will be known only when an empirical crystallographic structure becomes available for DnaC.</ref>. | ||
Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). The uncertainty in three of these regions is explained by gaps in the template model (see below). Although the details of these regions are even more uncertain than other regions, it seems likely that these loops are on the surface, if the homology model turns out to be substantially correct. | Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). The uncertainty in three of these regions is explained by gaps in the template model (see below). Although the details of these regions are even more uncertain than other regions, it seems likely that these loops are on the surface, if the homology model turns out to be substantially correct. | ||