I don't have a particular solution in mind, but wish to note that,
in my experience, something like this near a ASN or ASP residue is not
"unusual electron density". I have seen ugly density that looks like
this many times. I usually end up with partially occupied water
molecules, but am never happy with that solution.
Perhaps someone should do a survey of ASN residues in the PDB and
see what the very high resolution/high quality models say?
Dale Tronrud
On 7/22/2022 4:37 AM, Eleanor Dodson wrote:
It is hard to see from a still but there couldn't be another residue
there, could there? Tak the main chain through the ASN side chain, ASN
side chain uses some density - then fit residue X into the excess??
Eleanor
On Thu, 21 Jul 2022 at 12:44, Schreuder, Herman /DE
<herman.schreu...@sanofi.com <mailto:herman.schreu...@sanofi.com>> wrote:
I was also thinking of glycosylation, but as far as I know, E.coli
does not glycosylate protein. ____
Best,____
Herman____
__ __
*Von:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *Emmanuel Saridakis
*Gesendet:* Donnerstag, 21. Juli 2022 12:14
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* Re: [ccp4bb] Unusual electron density at ASN residue____
__ __
Hi, have you checked for partial N-linked glycosylation? It's an
obvious site for this, although difficult to explain the density
being at both sides of the ASN (maybe disorder) ?____
Emmanuel____
------------------------------------------------------------------------
*From: *"Nika Žibrat" <nika.zib...@ki.si <mailto:nika.zib...@ki.si>>
*To: *"CCP4BB" <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
*Sent: *Wednesday, 20 July, 2022 16:58:49
*Subject: *Re: [ccp4bb] Unusual electron density at ASN residue____
__ __
The crystallization condition is (NH_4 )_2 SO_4 _, glycerol and
2-Propanol. The distance between the residue the last visible
histidine (4 out of 6His) on the C-terminus is 12.5 Angstroms.____
____
Thank you, ____
Nika ____
____
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
*Reply to: *Jon Cooper <jon.b.coo...@protonmail.com
<mailto:jon.b.coo...@protonmail.com>>
*Date: *Wednesday, 20 July 2022 at 15:36
*To: *"CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>"
<CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject: *Re: [ccp4bb] Unusual electron density at ASN residue____
____
Hello, what is the crystallisation condition and cryoprotectant? I
am thinking it might just be poorly defined waters. Also, roughly
how close is the Asn to the most C-terminal residue in the structure
in Angstroms?
Best wishes, Jon.C.
Sent from ProtonMail mobile
-------- Original Message --------
On 20 Jul 2022, 13:39, Nika Žibrat < nika.zib...@ki.si
<mailto:nika.zib...@ki.si>> wrote: ____
____
Dear CCP4bb community, ____
____
I have a question on which I would greatly appreciate your
advice.____
I have solved 25 kDa protein structure at 1.7 A resolution with
molecular replacement. The protein was expressed heterologously
in E. Coli BL21 (DE3). There is a large uninterrupted electron
density on the ASN residue at the C-terminus of my protein (see
two images below). The density is extended from both nitrogen
and oxygen atoms. The FOFCWT density on the oxygen dissapears
at 5.5 rmsd and the one on the nitrogen side dissapears at 6.3
rmsd. ____
On C-terminus there are 12 aminoacids after this particular Asn
residue, six of which is 6xHIS tag. There are two molecules in
the ASU but this density is present only in molecule B.____
____
Any input on how to proceed regarding this density would be
appreciated.____
____
Best regards, ____
Nika ____
____
____
____
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