Quoting Andrew Purkiss-Trew <[log in to unmask]>:
> Quoting "Critton, David" <[log in to unmask]>:
>
>> Dear CCP4BB,
>>
>> I am building a protein structure containing a pair of cysteines
>> linked via disulfide bond. This disulfide bond (i.e. the cysteine
>> S-gamma atoms) refines well at 2/3 occupancy, however the electron
>> density suggests that these cysteines each adopt a second, unlinked
>> conformation (presumably at 1/3 occupancy). I have no trouble
>> building the alternate conformers; however, refinement causes both
>> conformers to disulfide-bond.
>>
>> I would like to know if there is a way (and how) to specify
>> individual conformers (or individual atoms) in the SSBOND record of
>> a PDB.
>>
>
Having seen Garib's response, the SSBOND record was probably a LINK
when I was refining the structure. I will check tomorrow if this was
the case.
> In a structure I refined a few years back, I had a similar
> situation, with Cys 18 partially disulphide bonded to Cys 22 in one
> chain (of two). In the case, the whole loop (plus one residue either
> side) between the CYS was modelled with two conformations. The
> structure was refined with Refmac version 5.2.0019 and the pdb code
> is 2V2U, if you are interested.
>
> From this file, the SS Bond record is
>
> SSBOND 1 CYS A 18 CYS A 22 1555
> 1555 2.05
>
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