We have determined the structures of some proteins we want our mutants to express. Others could be homology modelled due to existing 3D models that had high similarity to the ones we are working with.

Contents 1 Mutant 1 1.1 AMO 1.2 Hao 1.3 Cc554 1.4 Ccm552 2 Mutant 2 2.1 NirS 2.2 NirM 2.3 NOR

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 [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

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

Cc554

Cytochrome c554

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

Ccm552

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

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

NirM

Cytochrom c551

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

NOR

Flavorubredoxin

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] which was easily compiled and installed using an [http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install installation script] made by Troels Linnet.