Yes, exactly, those two proteins. Were you involved?
JPK
From: Clement Angkawidjaja [mailto:clem...@evec.jp]
Sent: Monday, November 14, 2016 12:42 AM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate
Maybe the Ca is just there as an additional binding site
Maybe the Ca is just there as an additional binding site for carbonate.
Btw, are you looking at CmpA/NrtA?
Cheers,
Clement
From: Keller, Jacob
Sent: Friday, November 11, 2016 2:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate
Well, I was looking at two
Once again, chemical intuition may help. At neutral pH values, sulfate
is going to be present at SO4(2-), whereas phosphate will be present as
H2PO4(-) or HPO4(2-). The hydrogen bond network supporting binding may
be able to offer clues. Sulfate is not likely to have any H-bond
acceptors in its
Assuming it wasn't clear from purification/crystallisation reagents...
Maybe try a high multiplicity anomalous dataset collected in house / at
long wavelength?
P has ~ 75% the f" of S at CuKa.
If you can figure out roughly what anomalous peak height an S atom gives
from a Cys or a Met with simil
Similarly, how do you differentiate a phosphate ion than sulfate just based
on electron density if data is not at atomic resolution?
Thanks!
On Fri, Nov 11, 2016 at 3:52 AM, Harry Powell
wrote:
> Hi all
>
> Sticking to the first question, if you don't restrict yourself to _X-ray_
> crystallogr
Hi all
Sticking to the first question, if you don't restrict yourself to _X-ray_
crystallography but use your local neutron source instead, it should be
straightforward (subject to all the normal caveats).
On 10 Nov 2016, at 23:02, Tim Gruene wrote:
> Dear JPK,
>
> to answer your first questi
, Jacob<mailto:kell...@janelia.hhmi.org>
Sent: Friday, November 11, 2016 5:41 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Nitrate versus Carbonate
Dear Crystallographers,
I don’t think there is any feasible way crystallographically to distinguish
between
Sent: Friday, November 11, 2016 5:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Nitrate versus Carbonate
Dear Crystallographers,
I don’t think there is any feasible way crystallographically to distinguish
between nitrate and carbonate or bicarbonate—correct? But that is not my main
Bicarbonate ion is a weak base and is normally protonated near neutral pH.
(Nitrate is a pathetically weak base and is not protonated at any
reasonable biological pH.) Therefore, bicarbonate will have one hydrogen
bond donor group (the -OH group) and two hydrogen bond acceptor groups,
whereas nitra
Dear JPK,
to answer your first question, at atomic resolution you would notice a density
difference between N and C. At a little less resolution you might still
measure difference in bond length.
Regrds,
Tim
On Thursday, November 10, 2016 8:41:43 PM CET Keller, Jacob wrote:
> Dear Crystallog
Keller,
Jacob
Sent: Thursday, November 10, 2016 3:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Nitrate versus Carbonate
Dear Crystallographers,
I don't think there is any feasible way crystallographically to distinguish
between nitrate and carbonate or bicarbonate-correct? But that is n
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate
If I had to speculate, the polarity vector vs. atomic geometry would be the
difference to utilize. The pKa of carbonate is around 6.3 for the first oxygen,
so at physiological pH I would assume the majority of carbonate is in the
Dear Crystallographers,
I don't think there is any feasible way crystallographically to distinguish
between nitrate and carbonate or bicarbonate-correct? But that is not my main
question.
My main question is: given that nitrate and carbonate are both very important
and also very different phys
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