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 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 which was easily compiled and installed using an installation script made by Troels Linnet.