Difference between revisions of "Part:BBa K1033906"
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[[Image:ts purple swiss.png]]
 
[[Image:ts purple swiss.png]]
  
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−
 
−
<!-- -->
 
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QMEANnorm = 0.02
 
−
<br>Cβ = -0.91
 
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<br>All Atom = 0.52
 
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<br>Solvation = -1.19
 
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<br>Torsion = 0.32
 
  
  
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<br><strong>Plot 3</strong>
 
<br><strong>Plot 3</strong>
 
<p>The analysis of these Z-scores of the individual terms can help identifying the geometrical features responsible for an observed large negative QMEAN Z-score. Models of low quality are expected to have strongly negative Z-scores for QMEAN but also for most of the contributing terms. Large negative values correspond to red regions in the color gradient. "Good structures" are expected to have all sliders in the light red to blue region.”</p>
 
<p>The analysis of these Z-scores of the individual terms can help identifying the geometrical features responsible for an observed large negative QMEAN Z-score. Models of low quality are expected to have strongly negative Z-scores for QMEAN but also for most of the contributing terms. Large negative values correspond to red regions in the color gradient. "Good structures" are expected to have all sliders in the light red to blue region.”</p>
 +
 +
 +
<p>The QMEAN6 score is a composite score consisting of a linear combination of 6 terms (estimated model reliability between 0-1). The pseudo-energies of the contributing terms are given below together with their Z-scores with respect to scores obtained for high-resolution experimental structures of similar size solved by X-ray crystallography:</p>
 +
 +
 +
 +
<!-- -->
 +
<table border="1">
 +
<tr>
 +
<th>Scoring Function Term</th>
 +
<th>Raw Score</th>
 +
<th>Z Score</th>
 +
</tr>
 +
<tr>
 +
<td>Cβ Interaction Energy</td>
 +
<td>-31.74</td>
 +
<td>-1.36</td>
 +
</tr>
 +
<tr>
 +
<td>All Atom Pairwise Energy</td>
 +
<td>-17397.90</td>
 +
<td>-1.13</td>
 +
</tr>
 +
<tr>
 +
<td>Solvation Energy</td>
 +
<td>-87.05</td>
 +
<td>-0.09</td>
 +
</tr>
 +
<tr>
 +
<td>Torsion Angle Energy</td>
 +
<td>-244.66</td>
 +
<td>0.07</td>
 +
</tr>
 +
<tr>
 +
<td>Secondary Structure Agreement</td>
 +
<td>86.8%</td>
 +
<td>0.98</td>
 +
</tr>
 +
<tr>
 +
<td>Solvent Accessibility Agreement</td>
 +
<td>79.6%</td>
 +
<td>-0.10</td>
 +
</tr>
 +
<tr>
 +
<td>QMEAN6 score</td>
 +
<td>0.751</td>
 +
<td>-0.05</td>
 +
</table>
  
  
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<br>Grand average of hydropathicity (GRAVY): -0.395
 
<br>Grand average of hydropathicity (GRAVY): -0.395
 +
 +
 +
 +
===References===
 +
<p>1. Benkert, P., Schwede, T. and Tosatto, S.C.E. (2009). QMEANclust: Estimation of protein model quality by # combining a composite scoring function with structural density information. BMC Struct Biol. 2009 May 20;9:35. If you publish results using DSSP, please cite the following paper:
 +
Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features, Biopolymers 22:2577-2637</p>
 +
<p>2. Benkert P, Biasini M, Schwede T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics, 27(3):343-50.</p>
 +
<p>3. Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</p>

Revision as of 14:45, 3 October 2016

tsPurple, purple chromoprotein

This chromoprotein (also known as TinselPurple) naturally exhibits strong purple color when expressed.

Usage and Biology

This part is useful as a reporter.

AmilCP and tsPurple.jpg

iGEM2013 Uppsala: The images above show E coli constitutively expressing the chromoproteins amilCP BBa_K592009 and tsPurple BBa_K1033906 from the high copy plasmid pSB1C3 from the promoters J23116 and J23110.


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
    COMPATIBLE WITH RFC[1000]



Structure and SWISS MODEL Homology Modelling Report

(The following information has been contributed by SVCE_Chennai 2016)

The following sections give a detailed information on this chromoprotein done by its in silico analysis.



3D Structure

Ts2.gif



Cartoon representation of tsPurple.

Ts purple swiss.png



The best match during structure prediction.

Template Seq. Identity Oligo-state Found by Method Resolution Seq Similarity Range Coverage Description
4ohs.1.A 86.61 homotetramer HHblits X-Ray 2.19Å 0.58 2 - 222 0.98 FAR-RED FLUORESCENT PROTEIN AQ143


What about Ligands?

Ligand Added to Model Description
CL ✕ - Not biologically relevant. CHLORIDE ION
CL ✕ - Not biologically relevant. CHLORIDE ION
CL ✕ - Not biologically relevant. CHLORIDE ION



Plot 1

Tsp2.png


Plot 2

Tsp.png



Plot 3

Tsp3.png



Tsp4.png




Plot 1

The area built by the circles colored in different shades of grey in the plot on the left hand side represent the QMEAN scores of the reference structures from the PDB. The model's QMEAN score is compared to the scores obtain for experimental structures of similar size (model size +/- 10%) and a Z-score is calculated. A Z-score (or standard score) is a score which is normalised to mean 0 and standard deviation 1. Thus the QMEAN Z-score directly indicates how many standard deviations the model's QMEAN score differs from expected values for experimental structures. In analogy, Z-scores are calculated for all four statistical potential terms as well as the agreement terms being part of the QMEAN score.



Plot 2

The plot in the middle shows the density plot (based on the QMEAN score) of all reference models used in the Z-score calculation. The location of the query model with respect to the background distribution is marked in red. This plot basically is a "projection" of the first plot for the given protein size. The number of reference models used in the calculation is shown at the bottom of the plot.



Plot 3

The analysis of these Z-scores of the individual terms can help identifying the geometrical features responsible for an observed large negative QMEAN Z-score. Models of low quality are expected to have strongly negative Z-scores for QMEAN but also for most of the contributing terms. Large negative values correspond to red regions in the color gradient. "Good structures" are expected to have all sliders in the light red to blue region.”


The QMEAN6 score is a composite score consisting of a linear combination of 6 terms (estimated model reliability between 0-1). The pseudo-energies of the contributing terms are given below together with their Z-scores with respect to scores obtained for high-resolution experimental structures of similar size solved by X-ray crystallography:


Scoring Function Term Raw Score Z Score
Cβ Interaction Energy -31.74 -1.36
All Atom Pairwise Energy -17397.90 -1.13
Solvation Energy -87.05 -0.09
Torsion Angle Energy -244.66 0.07
Secondary Structure Agreement 86.8% 0.98
Solvent Accessibility Agreement 79.6% -0.10
QMEAN6 score 0.751 -0.05


Ramachandran Plot- SWISS MODEL Workspace

(The following information has been contributed by SVCE_Chennai 2016)


File:Ramaplot tspurple.pdf


A score of 93.3% in the most favoured regions as seen in the Ramachandran plot shows that the above predicted model of Tinsel Purple chromoprotein is a very good prediction.


ProtParam Results

(The following information has been contributed by SVCE_Chennai 2016)


Number of amino acids: 228
Molecular weight: 25546.26
Theoretical pI: 6.65
Total number of negatively charged residues (Asp + Glu): 27
Total number of positively charged residues (Arg + Lys): 26


Atomic composition:


Carbon (C) - 1134
Hydrogen (H) - 1747
Nitrogen (N) - 303
Oxygen (O) - 334
Sulfur (S) - 18



Formula: C1134H1747N303O334S18
Total number of atoms: 3536



Extinction coefficients:


Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.


Ext. coefficient : 24910
Abs 0.1% (=1 g/l): 0.975, assuming all pairs of Cys residues form cystines


Ext. coefficient : 24410
Abs 0.1% (=1 g/l): 0.956, assuming all Cys residues are reduced


Estimated half-life:


The N-terminal of the sequence considered is M (Met).


The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).


Instability index:


The instability index (II) is computed to be 31.19
This classifies the protein as stable.



Aliphatic index: 61.97


Grand average of hydropathicity (GRAVY): -0.395


References

1. Benkert, P., Schwede, T. and Tosatto, S.C.E. (2009). QMEANclust: Estimation of protein model quality by # combining a composite scoring function with structural density information. BMC Struct Biol. 2009 May 20;9:35. If you publish results using DSSP, please cite the following paper: Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features, Biopolymers 22:2577-2637

2. Benkert P, Biasini M, Schwede T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics, 27(3):343-50.

3. Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.