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Team:DTU-Denmark/Protein Models
From 2013.igem.org
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| - | *All homology models were made using the free | + | *All homology models were made using the free online tool [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels v3.2] |
*All models were made and visualized in [http://sourceforge.net/projects/pymol/ PyMOL v1.6] | *All models were made and visualized in [http://sourceforge.net/projects/pymol/ PyMOL v1.6] | ||
Revision as of 22:21, 1 October 2013
Protein Models
It turns out that the structures of some of the proteins we want our mutants to express have been determined.
Contents |
Mutant 1
AMO
Ammonia monooxygenase
homology models of all three subunits of AMO
At the time of writing neither of the the three subunits from Nitrosomonas Europae is available as 3D structures, so each of the subunits was identified at UNIPROT, and their sequence was homologymodelled using CPHmodels-3.2
| Resource | AmoA | AmoB | AmoC |
|---|---|---|---|
| Uniprot | Q04507 | Q04508 | Q82T63 |
| Template pdb code and chain | 1YEW.A | 1YEW.B | 3RGB.C |
| Coverage | 90.5 | 86.2 | 66.4 |
| E-value | 1e-87 | 3e-67 | 8e-43 |
The three subunits were combined and aligned to the subunits of the Crystal structure of particulate methane monooxygenase, hence an overlap of two alpha helices.
Hao
Hydroxylamine oxidoreductase
source 1FGJ
Cc554
Cytochrome c554
source 1FT5
Ccm552
Homology model of Ccm552
| Resource | Ccm552 |
|---|---|
| Uniprot | Q50926 |
| Template pdb code and chain | 2J7A.O |
| Coverage | 68.3 |
| E-value | 6e-11 |
Mutant 2
NirS
Nitrite reductase
As a dimer with N2 - source 1NNO
NirM
Cytochrom c551
source 2EXV
NOR
Flavorubredoxin
Homology model of NOR
| Resource | NOR |
|---|---|
| Uniprot | Q46877 |
| Template pdb code and chain | 1YCF.A |
| Coverage | 82.5 |
| E-value | 3e-95 |
- All homology models were made using the free online tool CPHmodels v3.2
- All models were made and visualized in PyMOL v1.6
