> My question is - is it necessary that we deposit a structure, which
> PISA predicted as most probable assembly in PDB as an
> asymmetric unit & biological assembly or can we deposit a dimer
> (asymmetric unit) and give explanation for the biological assembly
> according to what PISA predicted.
>
As others have said - you are free to deposit whatever model you believe
is consistent with your experimental data. If we assume that you know
what the biological assembly is (see below), you still may (and people
do that) deposit a different arrangement - it's not wrong per se, but
think about non-structural folk (there should be a better word) that
will look at your deposited model and may not have the experience to
realize what they are looking at.
> Other than such predictions what other criteria needs to be
> considered to say that one specific assembly is a biological assembly?
>
1. You need to show that your protein is a dimer in solution.
Gel-filtration (sometimes problematic), dynamic light scattering (often
problematic), analytical ultracentrifugation (less problematic but
instruments are not widely available) as well as methods I mention in 2
are useful here.
2. You need to show somehow that the dimer you see in crystal is the
same as dimer in solution. Many approaches are available here - I am a
recent SAXS convert, and I wholeheartedly recommend that, but your
mileage may vary. SAXS will also unequivocally determine the
oligomerization state. Cross-linking and HD exchange, both in line of
mass-spectrometry, are good ways to get it done too.
With that said, you may be able to get away with just the crystal
structure assuming that the PISA results are convincing (e.g. you have
one heavily hydrophobic interface that is large enough and much larger
than any other more polar alternatives.
> Another question-
> In this case one of the chain has 3 MSE residues, while the other
> chain has only 2 MSE (When we change MET to MSE, there will be a
> huge negetive density coming up).
>
This is rather curious. While it's definitely possible that your
protein prep had variable incorporation ratio, the fact that you see it
in a specific spot seems to suggest that selenium slightly alters the
structure directing the crystallization.
> Are there any such instances in PDB, where two homodimer (or any mer)
> will have different percentage of MSE?
>
Hopefully someone knows the answer, but you can always just mine the
database.
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
