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 <epozh...@umaryland.edu> wrote: > From: Ed Pozharski <epozh...@umaryland.edu> > Subject: Re: [ccp4bb] PEG in the pdb? > To: CCP4BB@JISCMAIL.AC.UK > 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 >
