That's a good point, Ed
Based on the formula: HO CH2-(CH2-O-CH2)n-CH2OH, PEG MW = 44n+62, a table of n to MW goes like below which gives an idea of what range is possible. Someone maybe knows what polydispersity can be expected from the synthetic process. As you say though, a specific range could partition out of the bulk to the protein surface. And the main point of the original post was that only a subset of atoms in the bound PEG may be ordered enough to see.
n MW
5, 282.
6, 326.
7, 370.
8, 414.
9, 458.
10, 502.
11, 546.
12, 590.
13, 634.
14, 678.
15, 722.
16, 766.
17, 810.
18, 854.
19, 898.
20, 942.
21, 986.
22, 1030.
23, 1074.
24, 1118.
25, 1162.
26, 1206.
27, 1250.
28, 1294.
29, 1338.
30, 1382.
31, 1426.
32, 1470.
33, 1514.
34, 1558.
35, 1602.
36, 1646.
37, 1690.
38, 1734.
39, 1778.
40, 1822.
41, 1866.
42, 1910.
43, 1954.
44, 1998.
45, 2042.
46, 2086.
47, 2130.
--- On Thu, 12/8/10, Ed Pozharski <[log in to unmask]> wrote:
> From: Ed Pozharski <[log in to unmask]>
> Subject: Re: [ccp4bb] PEG in the pdb?
> To: [log in to unmask]
> Date: Thursday, 12 August, 2010, 17:35
> PEG solutions contain fragments of
> all sizes - it is the average size
> (however defined by the manufacturer) that is 1000.
> So technically it
> is incorrect to claim that you have PEG1000 molecules bound
> to your
> protein, it is most likely much shorter fragments that can
> penetrate the
> channels in protein crystals.
>
> It's not a lot of work to generate monomer libraries for
> peg fragments
> of different length (and some are available from standard
> monomer
> libs).
>
> I always wondered why PEG is not defined in the standard
> libraries as a
> polymer - perhaps because it is rarely needed. Or is
> it?
>
> Ed.
>
> On Thu, 2010-08-12 at 08:16 +0000, Klaus Sengstack wrote:
> > Hi everybody,
> >
> > I just solved the structures of an enzyme an some
> variants. In the
> > active site cavity of each variant I found one or two
> fragments of
> > PEG1000 bound. I used PEG1000 in the crystallization
> condition. Among
> > the enzyme variants the number of non-hydrogen atoms
> of these PEG
> > fragments varies between 7 and 19 atoms. Now I want to
> deposit the
> > structures in the pdb and my question is, if I have to
> define each
> > fragment as a single ligand (what would be a lot of
> work) or can I
> > define them as PEG1000 molecules? Thanks.
> >
> > K.S.
> >
> >
>
> --
> "I'd jump in myself, if I weren't so good at whistling."
>
>
> Julian, King of Lemurs
>
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