Difference between revisions of "Part:BBa K4165173"

Revision as of 18:24, 10 October 2022

Biobrick GST - CoH2 - Linker - WWW

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), GST (BBa_K4165070), CoH2 (BBa_K4165003), GGGGSx3 (BBa_K4165068), WWW (BBa_K4165007), and T7 terminator (BBa_K731721).

Source

Synthesized

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 45
Illegal SapI.rc site found at 189

=Dry Lab

Modeling

From 3 models out of 16 Models modeled in 4 software, 1 Model ranked best according to its Q_Mean values 4 and 6. The best Model has values of : score 5 out of 6 , C-Beta deviation = 1 , clash score = 3.08 , molprobitey = 1.35 , Ramachandran favored = 96.31, Ramachandran outlier = 0.79 , Q Mean_4 = -0.01 , Q_Mean_6 = -0.29.

                          Figure 1. The 3D structure of the COH-Linker-WWW model visualized by Pymol.

Mathematical modeling

Transcription rate and translation rate under T7 promotor

the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab.

                       Figure 1. this figure shows the results from the transcription and translation code showing the 
                            variation of mRNA and protein concentrations with time compared with the wet lab results.

@@ Line 4: / Line 4: @@
 This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), GST (BBa_K4165070), CoH2 (BBa_K4165003), GGGGSx3 (BBa_K4165068), WWW (BBa_K4165007), and T7 terminator (BBa_K731721).
+===Source===
+Synthesized
 <!-- Add more about the biology of this part here
 ===Usage and Biology===
 <!-- -->
 ===<span class='h3bb'>Sequence and Features</span>===
 <partinfo>BBa_K4165173 SequenceAndFeatures</partinfo>
+====Dry Lab===
+<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
+From 3 models out of  16 Models modeled in 4 software, 1 Model ranked best according to its Q_Mean values 4 and 6. The best Model has values of :
+score 5 out of 6 , C-Beta deviation = 1 , clash score = 3.08 , molprobitey = 1.35 , Ramachandran favored = 96.31, Ramachandran outlier = 0.79 , Q Mean_4 = -0.01 , Q_Mean_6 = -0.29.
+<html>
+<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/gst-coh-linker-www.png" style="margin-left:200px;" alt="" width="500" /></p>
+</html>
+                           Figure 1. The 3D structure of the COH-Linker-WWW model visualized by Pymol.
+<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
+<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
+the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab.
+<html>
+<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/clw2.png" style="margin-left:200px;" alt="" width="500" /></p>
+</html>
+                        Figure 1. this figure shows the results from the transcription and translation code showing the
+                             variation of mRNA and protein concentrations with time compared with the wet lab results.