Re: [ccp4bb] peroxy-glutamate?

Actually this is taken care of in the BIOMOLECULE definition. If the artist had used the principle biomolecule, it excludes the Fv fragments. On 05/09/2017 01:08 PM, Edward A. Berry wrote: In line with this, there are a number of pictures in the literature of the mitochondrial electron

Re: [ccp4bb] peroxy-glutamate?

In line with this, there are a number of pictures in the literature of the mitochondrial electron transport chain, with the complexes lined up in a row embedded in a membrane, and with yeast complex III still having the Fv fragments it was crystallized with, attached. Only obvious if you are

Re: [ccp4bb] peroxy-glutamate?

A slightly different wrinkle on the perennial "do we model unresolved sidechains" debate, I guess. I would argue that in the case of mutations, tags etc. those are things you know were there before you started firing x-rays at your sample. In the case of the sidechain decarboxylation we know

Re: [ccp4bb] peroxy-glutamate?

Hi Tristan I'm not so sure. The co-ordinates are the result of the experiment. How other people choose to interpret those results is their affair. Taking it to its logical conclusion suppose that we 'damage' the protein by mutating/deleting some residues or adding tags purely for the purpose

Re: [ccp4bb] peroxy-glutamate?

Hmm... this is a bit of a philosophical pickle in my mind. I agree. Right now I want as accurate a model as possible to improve the phases for interpretation of a few remaining bits. I haven't decided what to deposit- maybe three separate structures: 1. Conservatively modeled: Everything that

Re: [ccp4bb] peroxy-glutamate?

e done at some point anyway, now that we have the cyber-power to do it? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tristan Croll Sent: Tuesday, May 09, 2017 11:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate?

Re: [ccp4bb] peroxy-glutamate?

Hmm... this is a bit of a philosophical pickle in my mind. Do we want to model the structure as what it looks like after radiation damage has had its way with it, or what it must have looked like *before* the damage? I can see arguments both ways (and can sympathise with the former if you want

Re: [ccp4bb] peroxy-glutamate?

On 05/09/2017 06:18 AM, Ian Tickle wrote: We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So it's indeed very tempting to

Re: [ccp4bb] peroxy-glutamate?

Hi Jacob On 9 May 2017 at 14:03, Keller, Jacob wrote: > Wouldn’t the not-bonded CO2 have a new steric clash with the CG, though? > I think the CG can easily swing out of the way, since it's now only attached to the CB. > And what happened to the radical that was

Re: [ccp4bb] peroxy-glutamate?

@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Tuesday, May 09, 2017 6:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? Hi Andrew We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where

Re: [ccp4bb] peroxy-glutamate?

Hi Andrew We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So it's indeed very tempting to say that the CO2 is still there,

Re: [ccp4bb] peroxy-glutamate?

As you suggest, it depends on the contour level. Looking through a list of 17 dicarboxylates that I found problematic, there were 4 (actually two and their ncs-mates) that showed disconnected density for the carboxylate at 1.4 sigma as in the figure I sent. Going up to 2 sigma, four more

Re: [ccp4bb] peroxy-glutamate?

new sites, for the CO2 as well as for sulphurs. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of DUMAS Philippe (VIE) Sent: Thursday, May 04, 2017 6:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? Le Jeudi 4 Mai 2017

Re: [ccp4bb] peroxy-glutamate?

Le Jeudi 4 Mai 2017 12:25 CEST, Andrew Leslie a écrit: Dear Andrew, We looked in details to this problem of diffusion at ca. 100 K with bromine in "Ennifar et al., Acta D58(2002)1262" and we concluded "It was attempted to derive a value for the diffusion coefficient

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, I find your electron density quite interesting, because generally (I think, I would be happy to be corrected on this) when de-carboxylation of Asp/Glu occurs due to radiation damage, there is no evidence of what happens to the resulting CO2 group. One interpretation of

Re: [ccp4bb] peroxy-glutamate?

Damage-Selective (DamSel) map? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bellini, Dom Sent: Wednesday, May 03, 2017 6:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? or RDM (raddam detection map), better known as raddamap? :) BW, D

Re: [ccp4bb] peroxy-glutamate?

Dear Gerard, I am sure others > are certain to propose a cooler name for that very same type of map > some day ;-) . > a free tip: how about DDM (Decarboxylation Detector Map)? All the best, Pavel

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, Thank you for the picture. The decarboxylation of GLU and ASP side-chains is perhaps the most ubiquitous manifestation of radiation damage. We have introduced a feature in our autoPROC processing package whereby, if redundancy in the unmerged data is sufficient to allow reasonably

Re: [ccp4bb] peroxy-glutamate?

On 05/03/2017 02:46 PM, Gerard Bricogne wrote: Dear Ed, Have you considered the possibility that it could be a water stepping in to fill the void created by partial decarboxylation of the glutamate? That could be easily modelled, refined, and tested for its ability to flatten the

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, Have you considered the possibility that it could be a water stepping in to fill the void created by partial decarboxylation of the glutamate? That could be easily modelled, refined, and tested for its ability to flatten the difference map. Gerard. -- On Wed, May 03, 2017 at

Re: [ccp4bb] peroxy-glutamate?

Thanks to all who replied. Yes, in some of the other cases density between Cd and Cg is conspicuously weak. From preliminary tests it looks like dual conformations, in some cases together with correlated waters, will account for the density adequately. No Zebras here! eab On 05/03/2017 04:26

Re: [ccp4bb] peroxy-glutamate?

Peroxyacids are unlikely - they're very reactive/unstable under normal conditions. Is it possible your crystal is just at unusually low pH so these acids are protonated? That makes the carbon-oxygen bond lengths asymmetric, possibly by enough to explain your blobs. Tristan Tristan Croll