Difference between revisions of "Part:BBa K4165072"
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<partinfo>BBa_K4165072 short</partinfo>
 
<partinfo>BBa_K4165072 short</partinfo>
  
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This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS (BBa_K4165264), GST-tag (BBa_K4165070), DocS (BBa_K3396000), and T7 terminator (BBa_K731721).
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This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST-tag (BBa_K4165070), DocS (BBa_K3396000), and T7 terminator (BBa_K731721).
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===Source===
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Synthesized
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===Usage and Biology===
 
===Usage and Biology===
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<partinfo>BBa_K4165072 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165072 SequenceAndFeatures</partinfo>
  
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===Dry Lab===
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===Modeling===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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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
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Model “peptide (GST_DocS) modeled by Rosettafold full_model_407305_3” Ranked the fourth model from our 4 ones with a score 4 out of 6 and values of:
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<style>
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table, th, td {
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  border:1px solid black; margin-left:auto;margin-right:auto;
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}
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</style>
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<table style="width:65%">
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<table>
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  <tr>
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    <th>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>molprobity</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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    <td>0</td>
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    <td>182.78</td>
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    <td>2.72</td>
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    <td>98.25</td>
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    <td>0.7</td>
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    <td>0.75</td>
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    <td>1.02</td>
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  </tr>
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</table>
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                                 Figure 1. The 3D structure of GST-DOCs model Visualized by Pymol.
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                                 Figure 1. The 3D structure of the GST-DOCs model Displayed on Pymol.
  
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<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
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===Mathematical Modeling===
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promoter </p>
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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.  
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The mathematical modeling was based on our code for the calculation of transcription and translation according to thermodynamic laws and ODE (You can find it on our wiki) and compared the results with the wet lab.  
  
 
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               Figure 2. This figure shows the results from the transcription and translation code showing
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               Figure 2. this figure shows the results from the transcription and translation code showing
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     the variation of mRNA and protein concentrations with time compared with the wet lab results (1mM IPTG concentration)
 
     the variation of mRNA and protein concentrations with time compared with the wet lab results (1mM IPTG concentration)
  
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               Figure 3. this figure shows the results from the transcription and translation code showing
 
               Figure 3. 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 (2mM IPTG concentration)
 
     the variation of mRNA and protein concentrations with time compared with the wet lab results (2mM IPTG concentration)
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===WetaLab Results===
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/wetlab-results/gst-doc-pgs.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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                                  Figure 4. Transformed plate of GST Doc + pGS-21a
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<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Latest revision as of 11:12, 12 October 2022


T7 promoter-GST-DocS-T7 terminator

This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST-tag (BBa_K4165070), DocS (BBa_K3396000), and T7 terminator (BBa_K731721).

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

Modeling

Model “peptide (GST_DocS) modeled by Rosettafold full_model_407305_3” Ranked the fourth model from our 4 ones with a score 4 out of 6 and values of:

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 182.78 2.72 98.25 0.7 0.75 1.02 


                               Figure 1. The 3D structure of the GST-DOCs model Displayed on Pymol.

Mathematical Modeling

Transcription rate and translation rate under T7 promoter

The mathematical modeling was based on our code for the calculation of transcription and translation according to thermodynamic laws and ODE (You can find it on our wiki) and compared the results with 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 IPTG concentration)



              Figure 3. 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 (2mM IPTG concentration)