/dr-anthony-addlagatta-1
-- Original Message ---
From: Annemarie Weber
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, 3 Feb 2014 17:37:00 +0100
Subject: [ccp4bb] unexplained density
> ***
> This message has been scanned by the InterScan for CSC SSM at IICT and found
It looks like a Hepes?
Padayatti
On Mon, Feb 3, 2014 at 8:37 AM, Annemarie Weber <
annemarie.we...@uni-konstanz.de> wrote:
> Dear all,
> I am refining a 1.4 A resolution structure and found some well-defined but
> unfortunately unexplained density. The protein was purified in HEPES buffer
> with
What does anomalous difference Fourier look like?
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Annemarie
Weber
Sent: Monday, February 03, 2014 11:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unexplained density
Dear all,
I am refining a
-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Annemarie Weber
[annemarie.we...@uni-konstanz.de]
Sent: Monday, February 03, 2014 6:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unexplained density
Dear all,
I am refining a
Hi MM,
Co in its +2 oxidation state typically forms a tetrahedrally coordinated
species in high pH environment; and pentagonally coordinated species with five
ligands at low pH. A Co ion in its +3 oxidation state forms a octahedrally
coordinated species with six ligands. Co +3 is unusual in bi
Are the imidazole rings of the histidines distorted? If they are, it could be
water/hydroxide. If not, it is probably a cobalt ion side show.
Cheers,
Rob Meijers
EMBL Hamburg
--- On Thu, 7/7/11, Artem Evdokimov wrote:
From: Artem Evdokimov
Subject: Re: [ccp4bb] Unexplained density near
Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion)
depending on the chemical environment...
Artem
On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian <
mach...@med.unc.edu> wrote:
> Y'all,
>
> I was wondering if anyone had any thoughts about a feature we observe w
We have a manganese binding protein that binds two Mn ions in a binuclear
complex. It turns out that one of the metal ions can move about 2.0 Å
depending on crystallization & data collection conditions (check out PDB files
1ON1 and 2F5D for the alternate conformations). In some instances we co
hey Mischa
I would guess that is a split cobalt/metal site occupancy 0.1 and 0.9 or
something like that.
If you calculate an anomalous difference map you may be able to confirm/reject
that suggestion, depending on the strength of the anomalous signal.
cheers
Preben
On 07.07.2011, at 17:07,
It could be a cacodylate bridging between two zincs. I would want to
know if anomylous maps show a third peak in the middle.
On 04/30/10 12:41, Maia Cherney wrote:
I think cacodilate is less likely because it's negatively charged as the
carboxy groups that surround the density.
I think it's Zn
I think cacodilate is less likely because it's negatively charged as the
carboxy groups that surround the density.
I think it's Zn or it may be another (endogenous) metal ion like Ca. You
need to look at the coordination.
Maia
David Schuller wrote:
The figures would be more helpful if you tol
The figures would be more helpful if you told us what each map contour
represented, and at what contour level. I assume blue is 2fo-fc and
green+red is fo-fc, positive and negative. It would be even more helpful
to have the maps to turn over in 3D, but I understand you would probably
be relucta
Hi,
Anomalous map might give you some idea if it can be zinc.
~L~
__
Lari Lehtiö
Pharmaceutical Sciences, Department of Biosciences
Åbo Akademi University,
BioCity, FIN-20520 Turku
Finland
+358 2 215 4270
http://www.users.abo.fi/llehtio/
_
Dear Daniel
Is the omit map for the model with and without the zinc ions possible to confirm
its existence? I am curious. What is the resolution of dataset?
stephen
Quoting Daniel Bonsor :
> Hello again
>
> I currently have some unexplained density in my structure. As you can
> hopefully see f
While it would not be unreasonable for zinc ions
to be coordinated to the asp residues (perhaps with bridging waters or
hydroxides), I am a little troubled by the lack of electron density
around the coordinating residues. If there are zinc ions tightly
coordinated at full occupancy, I would nor
I think it could be zinc ion.
On Fri, Apr 30, 2010 at 5:38 AM, Daniel Bonsor wrote:
> Hello again
>
> I currently have some unexplained density in my structure. As you can
> hopefully see from the images (see file), the density is dumbbell shaped.
> Whatever it is, it is coordinated by Asp and G
The close approach of the two Zinc atoms may not be too implausible if
the charges are being quenched by coordination of the negatively
charged residues.
William Ho
On Thu, Apr 29, 2010 at 5:38 PM, Daniel Bonsor wrote:
> Hello again
>
> I currently have some unexplained density in my structure
It's hard to see clearly the density, but judging from the abundance of
carboxy groups, it may be a metal.
Maia
Daniel Bonsor wrote:
Hello again
I currently have some unexplained density in my structure. As you can hopefully
see from the images (see file), the density is dumbbell shaped. Wha
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