Team:DTU-Denmark/Protein Models

From 2013.igem.org

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It turns out that the structures of some of the proteins we want our mutants to express have been determined.
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It turns out that the structures of some of the proteins we want our mutants to express have been determined. While others could be homology modelled due to existing 3D models that had high enough similarity to the ones that we are working with.
==Mutant 1==
==Mutant 1==
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===AMO===
===AMO===
Ammonia monooxygenase
Ammonia monooxygenase

Revision as of 22:23, 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. While others could be homology modelled due to existing 3D models that had high enough similarity to the ones that we are working with.

Contents

Mutant 1

AMO

Ammonia monooxygenase

DTU AMO.png

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 [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels-3.2]

Resource AmoA AmoB AmoC
Uniprot [http://www.uniprot.org/uniprot/Q04507 Q04507] [http://www.uniprot.org/uniprot/Q04508 Q04508] [http://www.uniprot.org/uniprot/Q82T63 Q82T63]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.A] [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.B] [http://www.pdb.org/pdb/explore/explore.do?structureId=3rgb 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 [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew Crystal structure] of particulate methane monooxygenase, hence an overlap of two alpha helices.

Hao

Hydroxylamine oxidoreductase

DTU Hao.png

source [http://www.rcsb.org/pdb/explore.do?structureId=1fgj 1FGJ]

Cc554

Cytochrome c554

DTU CycA.png

source [http://www.rcsb.org/pdb/explore.do?structureId=1ft5 1FT5]

Ccm552

DTU Cycx.png

Homology model of Ccm552

Resource Ccm552
Uniprot [http://www.uniprot.org/uniprot/Q50926 Q50926]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1j7a 2J7A.O]
Coverage 68.3
E-value 6e-11

Mutant 2

NirS

Nitrite reductase

DTU NirS NO.png

As a dimer with N2 - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=1nno 1NNO]

NirM

Cytochrom c551

DTU C551.png

source [http://www.rcsb.org/pdb/explore/explore.do?structureId=2exv 2EXV]


NOR

Flavorubredoxin

DTU NOR.png

Homology model of NOR

Resource NOR
Uniprot [http://www.uniprot.org/uniprot/Q46877 Q46877]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1ycf 1YCF.A]
Coverage 82.5
E-value 3e-95


  • 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]


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