Re: [ccp4bb] Post-translational modification induced strcture

On Thursday 04 March 2010 02:45:20 Miles Pufall wrote: > Dear All - > > Does anyone have some good examples where a post-translational modification > has induced local structure? > I'm particularly thinking of structure induced by the modification only and > not something > multi-step like a

Re: [ccp4bb] Question about modeling SAM into a protein structure

Yuan Cheng wrote: Hi everyone, I am trying to model a S-adenosylmethionine (SAM) molecule into the active site of a protein using the SAH (exists in the crystal structure) as the template. What I have already tried but failed so far are 1)Pymol: I loaded the pdbs of SAM and protein-SAH int

[ccp4bb] 答复: [ccp4bb] Post-translational modification induced strcture

I would recommend protein kinases as examples. Almost all the protein kinase activities are regulated by autophosphorylation. In the inactive form, the kinase subdomains are aligned so that ATP cannot reach the catalytic center of the kinase. The autophosphorylation causes the two subdomains of

Re: [ccp4bb] Question about modeling SAM into a protein structure

I presume you have a dictionary for both SAM and SAH? You need SAM at least to use COOT. My method is to calculate a difference map with the SAM density - xclude all atoms like SAH or waters which might overlap SAM, then manually grad the SAM to the right place and run real space refinement

Re: [ccp4bb] Post-translational modification induced strcture

Title: Re: [ccp4bb] Post-translational modification induced strcture Collagen probably isn't a great example as hydroxylation of proline in collagen enhances the thermal stability of collagen, it doesn't really "induce" collagen structure, as unhydroxylated (pro-pro-gly)n also form the canonical

Re: [ccp4bb] Trouble with P1 data

Twinning just requires some geometric relation between crystal axes to yes - it is possible in p1 othercell will tell you if there is some other indexing which will generate a similar arrangement of axes. It could be possible that it has higher symmetry of course. Eleanor José Trincão wrot

Re: [ccp4bb] density in LLG maps for heavy atoms sit on xtal axes?

It is common - errors seem to pile up there.. Eleanor Francis E Reyes wrote: Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pg

Re: [ccp4bb] Post-translational modification induced strcture

Hi Miles - I would say a good example of that phenomenon is collagen, where hydroxylation of the prolyl residues alows the polypeptide to adopt its helical conformation. In that case it is the fact there is an electronegative substituent on the prolyl ring that biases it into a particular conforma

[ccp4bb] arp_solvent ignores FreeR flag when run from ccp4i

Hi, I'm posting this here as I'm not sure if it's a problem with the ccp4i interface or ARP/wARP. When I run arp_solvent (version 7.1) from the ccp4i interface (6.1.2, ccp4i 2.0.5 from fink (32 bit) on OS X 10.6.2) whatever I set the "for REFMAC5 refinement do [not use/use] the Free R flag" t

[ccp4bb] Post-translational modification induced strcture

Dear All - Does anyone have some good examples where a post-translational modification has induced local structure? I'm particularly thinking of structure induced by the modification only and not something multi-step like a modification that recruits a cofactor that induces structure. Than