Agreed, it doesn't look like a zinc site, or indeed any metal site, with all
those basic residues around it, but just being a bad loser ;-0 Cheers, Jon.C.
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On 2 Jul 2022, 08:14, Eleanor Dodson wrote:
> Did you check anomalous
Did you check anomalous difference peaks? They would show zn very clearly.
On Sat, 2 Jul 2022 at 08:08, Sayan Saha wrote:
> Dear all,
> As suggested by most people, we modeled Zn2+ ions coordinated with
> three water molecules.
> Thanks for everyone’s response.
>
> With best regards,
>
Dear all,
As suggested by most people, we modeled Zn2+ ions coordinated with
three water molecules.
Thanks for everyone’s response.
With best regards,
Sayan Saha
On Fri, Jul 1, 2022 at 8:04 PM Jon Cooper
wrote:
> Hello, I wonder if it is disorder i.e. alternative conformations of the
> Asp
Hello, I wonder if it is disorder i.e. alternative conformations of the Asp and
flexible Lys.
Do let us know your final interpretation as we don't often, or indeed ever,
hear the final outcome of these mystery density competitions and I would love
to learn more from them.
Cheers, Jon.C.
Sent
Could it be Tris?
Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
From: CCP4 bulletin board on behalf of Sayan Saha
Sent: 30 June 2022 08:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified electron density
External Sender: Use caution.
Dear All,
I am trying to refine a protein structure. I observed an additional electron
Professor in Structural Biochemistry
University of Exeter
Living Systems Institute
Stocker Road
Exeter EX4 4QD
UK
From: CCP4 bulletin board On Behalf Of Sayan Saha
Sent: 30 June 2022 08:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified electron density
CAUTION: This email originated from
, 2018 09:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] unidentified electron density
>
> Dear All
>
> I am refining a 1.63 Angstrom data set for a methyltransferase for
> which methyl-accepting substrate is not known. I came across a density
> in the putative substrate
@JISCMAIL.AC.UK
> Subject: [ccp4bb] unidentified electron density
>
> Dear All
>
> I am refining a 1.63 Angstrom data set for a methyltransferase for which
> methyl-accepting substrate is not known. I came across a density in the
> putative substrate binding site in which i ha
board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
zaigham mahmood khan
Sent: Friday, July 06, 2018 15:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unidentified electron density blob
Hey Uma
Yes, you are right that PFPE is too big for this density. Also, more experienced
scientist in this field h
age-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> zaigham mahmood khan
> Sent: Friday, July 06, 2018 15:30
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Unidentified electron density blob
>
> Hey Uma
>
> Yes, you are right that PF
Hey Uma
Yes, you are right that PFPE is too big for this density. Also, more
experienced scientist in this field has already commented on it.
For the second part of your query, this is how one can generate the
"crystallographic information file" - .cif for the ligand of choice (in
case it is not
Hello,
a really molecule should show up also in the 2Fo-Fc type map. This
appears not to be the case.
So indeed it is likely that your density corresponds to some
alternate conformation of the surrounding residues present with low
occupancy. The glutamic acid
Thanks Zaighum, Artem, and Eleanor, for your replies.
@Zaighum: I could not find a pdb file for PFPE- it is not listed in common
ligand dictionaries of Refmac, Phenix or even HIC-Up server, or in general. It
is fairly big molecule to fit into this small cavity. Also I couldn't find any
protein
Hmm - is the refinement complete? Maybe the GLU on the right could be moved
to use some of that greenness?
I try to make all sensible corrections, then check blobs..
Eleanor
On 3 July 2018 at 04:22, zaigham mahmood khan
wrote:
> Uma, that is not something that we see regularly in the crystal
>
Uma, that is not something that we see regularly in the crystal structures.
But i never used PFPE either. So, you may try PFPE. If this is not PFPE,
then you may read the biology of the protein.
Also I can see green density, but these green blobs are devoid of blue
density. So i will be cautious.
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