[ccp4bb]: Damaged SS-bond

[Bart Hazes <bhazes@ualberta.ca>]

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Dear all,

We have a protein with an interesting pattern of damage to a disulphide bond.
A room temperature rotating anode dataset shows only a single conformation.
Synchrotron datasets show apparently two conformations of the disulphide bond;
the original and one in which one of the cysteines adopts a different X1
angle. Fitting the second conformation optimally in our 0.78 Angstrom map
places the sulphur approximately 2.4Angstrom form the other cysteine sulphur.
Too far for a covalent bond and too short for vanderWaals comfort. The density
is somewhat elongated and difference density suggest a split conformation in
the second X1 setting, eg 3 conformations for one cysteine; the original
disulphide bond, a second disulphide bond with different X1, and a third
conformation with a sulfur-sulfur distance of ~3.0 Angstrom. Still 3.0 is
quite a bit shorter than twice the vanderWaals radius of sulphur
(3.7Angstrom).

I was hoping some of you with a chemistry background could suggest what may be
going on. If a disulphide bond is broken by radiation, does one get two
sulphur radicals, or will one cysteine become negatively and the other
positively charged? If so, could such an ion pair adopt a shorter "ionic" bond
than the standard 3.7Angstrom vanderWaals distance? If so would 2.4 or 3.0
Angstrom be the more likely. It is hard to argue with the density at this
resolution but still the protein should follow proper stereochemistry. Any
hints are appreciated.

Bart

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Dept. of Medical Microbiology & Immunology
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