Re: [ccp4bb] Cys Lys bond?

[Spiller, Benjamin]

A similar bond is seen collagen;  Met-Lys sulfilimine.

Science  04 Sep 2009:
Vol. 325, Issue 5945, pp. 1230-1234

Not sure if it helps, but in collagen the bond is conserved and not due to 
radiation damage.

Ben Spiller








On Apr 18, 2018, at 5:40 AM, Jonathan Davies 
> wrote:

Dear All,

Thanks for all of the responses so far..

Mark - I don't think it's caused by radiation damage, although this is 
certainly a concern. Using only a small subset of images from the start of data 
collection still gives fairly clear density with no positive or negative peaks 
around the cys and lys.

Christian - I haven't used jligand before but that was nice and simple.. I 
think a simple link record may suffice here though.

Matthew - Definitely a weird bond, potentially the cys was oxidised first and 
the beam caused more weirdness, I really have no idea! Having said that, I 
don't think this is the cause (see above).

David - Thanks for the paper!
Focco - Thanks for the publication!

Paul - I tried the "Make link via Acedrg" route but had some issues (my model 
exploded).. I'll send you the details off list later! Cheers!

Jonathan



From: Jonathan Davies
Sent: 17 April 2018 18:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Cys Lys bond?

Dear CCP4BB,

I've recently solved a structure to 1.15 Angstrom which has extremely clear 
density for what appears to be a lysine covalently bound to a cysteine (S-N). 
The distance between the cys-S and lys-N is 1.8 A. I thought initially that 
there may be a methyl group between the two (based on this paper 
http://doi.org/10.1002/pro.2958) but there definitely isn't enough space.

Some more info:
The protein was purified from recombinant E. coli expression, standard buffers 
(Tris, NaCl).
Crystallisation condition contains sodium acetate and PEG.
The residues in question are not part of an active-site.

I have two questions:

Has anyone seen a cys that is involved in a sulfanamide bond with a lys?

How would one go about modeling this bond in a way that doesn't upset coot, 
refmac or PDB validation?

Thanks in advance!
Jonathan

[ccp4bb] Research Technician Vanderbilt University.

[Spiller, Benjamin]

Colleagues,
The Spiller lab in the Department of Pharmacology at Vanderbilt University is 
seeking a Research Assistant to assist Dr. Professor Spiller in his laboratory. 
The Spiller lab is a structural biology lab focused on infectious disease and 
the host’s immune response. The job requires a moderate ability to work 
independently but also involves working directly with Dr. Spiller and other lab 
members to help determine crystal structures. The candidate will be expected to 
interact professionally with other lab members. Preference will be given to 
applicants with experience in some of the following responsibilities.
Molecular Biology

  *   Design and create new protein constructs for crystallization trials.
  *   Optimize protein expression of new protein constructs.
Protein Purification

  *   Design and carry out experiments on the basis of discussed plans with Dr. 
Spiller
  *   Analyze chromatography experiments.
Crystallization

  *   Design and carry out high throughput crystallization trials
  *   Optimize crystallization conditions

Interested applicants should send a CV and cover letter to Ben Spiller.

benjamin.spil...@vanderbilt.edu





Ben Spiller
Associate Professor
Departments of Pharmacology
and Pathology, Microbiology, and Immunology
Vanderbilt University School of Medicine
office:  615-322-6766

[ccp4bb] position available

[Spiller, Benjamin]

Dear CCP4 Users,

We have an opening for one federally funded post-doctoral or staff scientist 
position for a structural biologist to study bacterial voltage-gated sodium 
channels.   The ideal candidate will be self-motivated, creative, organized, 
and experienced in crystallography.   The lab is a structural biology group 
within the department of Pharmacology at the Vanderbilt University medical 
center in Nashville, TN.

Nashville combines the features of a college town with those of a fairly large 
city.  Urban amenities include restaurants, museums, theatres, music, yet the 
cost of living is moderate and the city is very livable.

Please email questions, CV’s, and references to Ben Spiller


 

[ccp4bb] Structural Biology Post-Doctoral Position

[Spiller, Benjamin]

Dear CCP4 Users,

We have an opening for one federally funded post-doctoral position for a 
structural biologist or protein biochemist to study bacterial voltage-gated 
sodium channels.   The ideal candidate will be self-motivated, creative, 
organized, and experienced in crystallography or protein biochemistry.   The 
lab is a structural biology group within the department of Pharmacology at the 
Vanderbilt University medical center in Nashville, TN.

Nashville combines the features of a college town with those of a fairly large 
city.  Urban amenities include restaurants, museums, theatres, music, yet the 
cost of living is moderate and the city is very livable.

Please email questions, CV’s, and references to Ben Spiller: [EMAIL PROTECTED]