Tale of Two proteins

I work with two proteins. One of them is of bacterial origin and the other is from mammalian cells. The bacterial protein is nice and manipulative. The mammalian one is finicky and hates being manipulated. It especially hates being produced in E.coli cells, the workhorse of molecular biology.
Therein lies the problem.

I express both the bacterial and the mammalian protein in E.coli. The bacterial protein is produced in tons of amounts and is easy to purify. I use it produce the inhibitor. The only unknown thing, and therefore of interest, in this entire process is the structure of the inhibitor. We have managed, after two months, to produce enough for NMR. Will I get the structure? That is something I do not have confidence in.

The mammalian protein is the one which is of tremendous interest. The inhibitor binds to it in an allosteric site and blocks its activity. I need to get at the structure of the protein. But the protein is so difficult to purify and concentrate that in these two months I have just managed to standardize conditions to purify and concentrate it.

With all the proteins being overexpressed in E.coli, lot of technique is mumbo-jumbo. We really do not understand. How does the plasmid get into the bacteria? Why does the bacteria retain some plasmids and throws others out? Why some proteins are produced in large amounts and why some are produced in tiny amounts? We can theorize. This is toxic, this is eukaryotic, this is that, this is that...but, honestly, that is lots of handwaving. We just have to accept what we get.