Re: [ccp4bb] Inclusion bodies centrifugation

What this indicates is that your protein is not in 'real inclusion bodies' but is merely precipitating - it's not even necessarily true that it's a precipitate inside the cell - instead it could be falling out of solution as you're lysing and so forth. It also may be binding to nucleic acids and th

Re: [ccp4bb] Supplementary density

Dear Fabien, Cases like that crop up from time to time. You shouldn't treat this peptide in any way differently than any other peptide. If you're reasonably sure about the peptide's sequence - BLAST it against a wide database (nr for example). Like others pointed out, just make sure that it's not

[ccp4bb] Post-doctoral position

Dear all -- please find here an announce for a post-doctoral position in this wonderful country that is Japan. Hope to see many of you applying. Kind regards -- Leo -- ### STARTS HERE ### Post-doctoral position. Structural Biology Research Center, Tsukuba, Japan [Closing date] All docu

Re: [ccp4bb] Supplementary density

Just a small note of caution: It's not a bit of vector-derived sequence is it? A bit of peptide linker between the protein of interest and any purification tags maybe? I know of at least one case where a piece of vector derived sequence has been present in the crystal (and in fact been critical fo

Re: [ccp4bb] Supplementary density

Fabien, The extra density may be from a his-tag or cloning artifacts left over at the beginning or end of your protein sequence. You may be seeing the residues coming from a neighboring molecule. I have seen parts of a C-terminal his-tag ordered in the electron density before. Jon Schuermann

Re: [ccp4bb] Supplementary density

Hi Fabien, Quinoprotein methanol dehydrogenase was supposed to contain only one subunit when it was discovered. Then 3D structure determination indicated the presence of a second, small subunit. See Nunn, Day & Anthony, Biochem J. 1989 June 15; 260(3): 857–862. Perhaps this is relevant. H

[ccp4bb] Postdoctoral Position at the MRC-LMB, Cambridge

Please be informed of the following position for a postdoctoral scientist at the LMB in Cambridge, UK. Postdoctoral Scientist £25,622 – £27,223 per annum The MRC Laboratory of Molecular Biology (LMB) is a world famous institution with a strong track record in train

Re: [ccp4bb] Supplementary density

Wow, you're lucky. The problem usually is to not have density for a peptide when one desperately wants density. ;-) You should treat this peptide just like you would any other. Build what you can see, and verify that the peptide obeys standard geometry, phi/psi plots, etc. It should have p

[ccp4bb] Supplementary density

Hello We’re resolving a structure of a soluble protein and in the electronic density map (maximum resolution at 2.2Å), we observe a supplementary density that does not belong to the protein. This density is present in two different crystalline forms obtained in different crystallization condi

Re: [ccp4bb] Crystalization of membrane proteins with lipids

Hi Radovan, you can look at "A Lipidic-Sponge Phase Screen for Membrane Protein Crystallization" Wöhri, A. B., Johansson, L. C., Wadsten-Hindrichsen, P., Wahlgren, W. Y., Fischer, G., Horsefield, R., Katona, G., Nyblom, M., öberg, F., Young, G., Cogdell, R. J., Fraser, N. J., Engström, S. &

Re: [ccp4bb] observations support

effectivement. merci JL cedric bauvois wrote: > Dear All > > Does anyone know a software which can help to annotate observations in > a crystallization experiment ? > > Thanks in advance, > > Regards > > Cédric > > > -- > .. > Dr.

Re: [ccp4bb] Crystalization of membrane proteins with lipids

Radovan Spurny wrote: I would like to ask for recommendations and tips how to use lipids for crystallization of membrane proteins. Especially I am interested about the solubilization of lipids (E.coli lipids, POPC, POPE, POPG) and how to mix them with protein. Thanks a lot. Have a look at:

[ccp4bb] modelling and refining a DNA phosphorothioate backbone

Hello, I have a DNA substrate in which only a few of the backbone phosphate linkages have been replaced with a phosphorothioate analog.� Currently, I can make a .cif file for the bases that have the replacement, but after running refinement in REFMAC5, the bases are not connected to the rest of

Re: [ccp4bb] Inclusion bodies centrifugation

Tried out the method, but our protein is also lost in the supernatant. i collected the supernatant after 1st centrifugation and centrifuged it to obtain the pellet. we observed that our protein is present in that pellet and in further washes also we see protein loss too. Thanks anyways for all the

[ccp4bb] observations support

Dear All Does anyone know a software which can help to annotate observations in a crystallization experiment ? Thanks in advance, Regards Cédric -- .. Dr. Cedric Bauvois Cristallographie des protéines Institut de Recherches Micr

[ccp4bb] Crystalization of membrane proteins with lipids

I would like to ask for recommendations and tips how to use lipids for crystallization of membrane proteins. Especially I am interested about the solubilization of lipids (E.coli lipids, POPC, POPE, POPG) and how to mix them with protein. Thanks a lot. R

[ccp4bb] Batch Queing of ccp4i Jobs

Dear all, has anybody set up successfully a batch queue for ccp4i under SUSE linux? Regards, Clemens