Difference between revisions of "Part:BBa K4165072"

Revision as of 04:00, 11 October 2022

T7 promoter-GST-DocS-T7 terminator

This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS (BBa_K4165069), GST-tag (BBa_K4165070), DocS (BBa_K3396000), and T7 terminator (BBa_K731721).

sOURCE

Synthesized

Usage and Biology

COH protein is a part of the Snitch system, which binds to the GST tag for the purification of the COH.

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

Model “peptide (GST_DocS) modeled by Rosettafold full_model_407305_3” Ranked fourth model from our 4 ones with score 4 out of 6 and values of C Beta deviation = 0 , clash score = 182.78 , molprobitey = 2.72 , Ramachandran favored = 98.25 , Ramachandran outlier = 0.7 , Q Mean_4 = 0.75 , Q Mean_6 = 1.02

                               Figure 1. The 3D structure of GST-DOCs 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 2. 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 (1mM on the left, 2mM on the 
                                                           right).

@@ Line 5: / Line 5: @@
 This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS (BBa_K4165069), GST-tag (BBa_K4165070), DocS (BBa_K3396000), and T7 terminator (BBa_K731721).
-<!-- Add more about the biology of this part here
+===sOURCE===
+Synthesized
 ===Usage and Biology===
+COH protein is a part of the Snitch system, which binds to the GST tag for the purification of the COH.
 <!-- -->
 ===<span class='h3bb'>Sequence and Features</span>===
 <partinfo>BBa_K4165072 SequenceAndFeatures</partinfo>
+===Dry Lab===
+<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
+Model “peptide (GST_DocS) modeled by Rosettafold full_model_407305_3” Ranked fourth model from our 4 ones with score 4 out of 6 and values of C Beta deviation = 0 , clash score = 182.78 , molprobitey = 2.72 , Ramachandran favored = 98.25 , Ramachandran outlier = 0.7 , Q Mean_4 = 0.75 , Q Mean_6 = 1.02
+<html>
+<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/gst-doc.png" style="margin-left:200px;" alt="" width="500" /></p>
+</html>
+                                Figure 1. The 3D structure of GST-DOCs 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/gst-doc2.png" "https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/gst-doc-2nm2.png"  style="margin-left:200px;" alt="" width="500" /></p>
+</html>
+               Figure 2. 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 (1mM on the left, 2mM on the
+                                                            right).