It could be purine or pyrimidine ring stacked between the Phe an Tyr. check pdb
3etr or 3eub of xanthine oxidase binding purine substrates between two Phe at
the active site.
Hongnan Cao
UCR
Date: Tue, 10 Feb 2009 00:23:54 -0500From: lvmengx...@gmail.comsubject:
[ccp4bb] unknown density fo
Dear all,
I have a crystal structure of a protein whose first 40 residues are in a
helical conformation. This helix was found to be bent, with the bend
occurring at residues 27-30, by an angle of roughly 60 deg . We believe
this bend was caused by crystal packing forces as this helix nicely
Sure, it's not always 'disastrously bad' to have EDTA (hence my use of the
word 'bad' rather than a more categorical statement. Donuts are bad for me
yet I can't stop eating them :)
Yes, you can take a risk. However since periplasmic isolation is already a
PITA, why add an extra concern?
Artem
>
Hi Mengxiao,
The density sure reminds me of a nucleotide.
Note the pi-pi stacking of the planar part
between Tyr and Phe, and in the third stereo
picture you attached, projections at what could
be the 2 and 6 positions remind me of Guanine...
plus there are Arg, Lys, etc. pointing toward
Hi everyone!
I have a problem when I use mlphare
Sure you do have a problem: you actually do use mlphare !
... with no intension to offend Eleanor's favorite program,
mlphare was a step forward in phasing, but about 20 years ago.
SHARP really put M(S)IR(AS) phasing in a new dimension, and SOL
I am trying to get a current version of ESCET to compare several models of
the same protein with different ligands.
I have tried twice to contact Thomas Schneider at the address listed in this
post:
>Hi,
>
>for obtaining ESCET, please contact me directly at:
>
>thomas.schnei...@embl-hamburg.de
>
>
Artem,
Artem Evdokimov wrote:
Please note that osmotic shock extraction typically employs EDTA which is
obviously bad for IMAC.
This is not entirely correct.
I have used extracts with 5 mM EDTA for IMAC in the past.
If your IMAC column volume is large enough, only the top 1-2 mm will be
dep
Hi,
If you could send in stereo mode of the density you want to get suggestion,
it will be convenient for the well trained eyes.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Feb 10, 2009 at 3:16 PM, wrote:
> Hi,
>
> It could be a
Hi,
It could be all sorts of things, but the one that for some reason is stuck
in my mind is isopentenyl phosphate (phosphate, not pyrophosphate!). Of
course w/o seeing the density in 3D this is just a guess.
Artem
> Dear All,
>
> When I was refining my structure, I found some unmodeled blobs, s
Dear all,
is there a progam(s) that compares cofactor or/and substrate binding site(s) in
the protein of interest with other already deposited protein structures? The
goal would be to find the structures with similar binding
sites/characteristics/.etc and maybe pointing to the putative functio
Dear Savvas,
Since you mention the case of TolC explicitly, I should add to what
Pietro Roversi has already written in his message in relation to anisotropy
effects. Ben Luisi's group kindly let us have their data in the late 20th
century, so that we could use the then new and exciting log-li
Hi,
I've just run some tests with Phaser-2.1.4 (the version distributed
with CCP4 6.1 and with Phenix-1.3-final), and I get a .rlist file when
running the brute rotation function. Could you send me the logfile
from your job (probably better to do this off-line) so I can see
whether it's
Dear Geoffrey,
it seems you read the manual
(http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC137),
but you didnt replace the imol and master-chain-id with a value. You
want to specify the molecule (imol, e.g. 0) and the chain from which to
copy to others (e.g. "A"),
Dear all,
one comment on the subject of white lines and anomalous phasing
power
- one has to be extremely careful to jump to conclusions
about the effect that a chemical treatment of the heavy atom (say
oxydation/reduction of Se) has
on the shape of the edge and the associated anomalous signa
Dear Mengxia,
the lower part could well be a sulfate ion. For the upper part, it is
difficult to guess from a static picture. Unfortunately, at the
resolution you have there are no programs which can build an unknown
small molecule from scratch according to the density. You have to guess,
fit it an
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