Re: help

CHOISET-Yvan (choiset@nantes.inra.fr)
Fri, 15 Mar 1996 12:31:42 -0800

UBCG25A@CCS.BBK.AC.UK wrote:
>
> hi yvan!
> good to hear from you.
> we know a number of peeple have trouble with regards connections and times
> for the MOO so that is why it is not required, but we still like to hear
> from you via email.
> you said you are finsihed with assignment 1 - what exactly do you mean by
> that - the self-assesment test or the analysis of the protein you were given?
> let me know so i can tell you how to proceed from here.
> have a good 2 week break
> cheers
> bonnie

Hello
Here what I mean

Start by inspecting/retrieving the relevant file(s) from
Brookhaven/PDB for me 4pti(proteinase inhibitor trypsin)P00974

1.Do there appear to be other codes in PDB which are closely related?
(Often there are entries of the form 1ABC, 3ABC, etc.)

2.Are there other proteins in PDB of the same name/functionality, but
from different species? Or mutants? Are there any with the same
protein composition by different non-protein constituents?

3.Does your protein contain:
(a) any water molecules? What percentage of the molecular
weight
(or molecular volume) are they? Why are they there?
(b) any other solvent?
(c) any counter-ions?
(d) any other small molecules?

4.Does your protein have any non-protein molecule bound to it? How?

5.Does your protein contain any disulphide bridges? Or any free -SH
groups?

6.Is there any ambiguity in your protein's composition in the PDB file?

7.How many molecules are there in your protein? Are there more reported
in PDB?

8.Does it have a SEQRES record? Does this correspond to the ATOM cards?

9.Is the crystal structure composed of discrete molecules? Or is there
evidence of oligomerisation? What symmetry does any oligomer have?

10.Is there any evidence **in the crystal** that the protein is not
homogeneous?

11.Is there a picture of your protein in PDB?

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Crystallography

12.What is the resolution of your crystal structure? The R-factor? Were
all atoms located? (Roughly) What are your temperature factors? Why
do
they matter? What is the spacegroup? (DON'T WORRY about
understanding
it).

Find the corresponding entry in SWISSPROT (species is
important!)

13.Does the SWISSPROT sequence correspond to the PDB sequence(s)? If
not,
why?

14.Does the protein have an entry in PROSITE?

15.Is there an entry in SWISS3DIMAGE?

16.What are the pI and MWt of your protein? (HINT: Use ExPAsY).

17.Has your protein undergone any processing?

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Find the corresponding entry in a nucleic acid database

18.Is your entry genomic or cDNA? Does it matter? Does it relate
directly
to the SWISSPROT sequence?

From all databases

19.What is known about the function of your protein? Are the databases
consistent? (Do not worry about relating function to structure at
this
stage).

Yvan