Quoting "Critton, David" <[email protected]>:
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.
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
There are also CONECT records for the two sulphurs in the conformation
(B) with the SS bond:
CONECT 162 214
CONECT 214 162
The coordinate records
ATOM 151 N ACYS A 18 -1.968 -5.316 4.592 0.50 30.47 N
ATOM 152 CA ACYS A 18 -2.372 -6.422 3.739 0.50 30.02 C
ATOM 153 C ACYS A 18 -1.903 -7.744 4.354 0.50 29.25 C
ATOM 154 O ACYS A 18 -0.937 -7.774 5.113 0.50 28.70 O
ATOM 155 CB ACYS A 18 -1.777 -6.254 2.339 0.50 29.88 C
ATOM 156 SG ACYS A 18 -2.490 -7.322 1.060 0.50 31.43 S
ATOM 157 N BCYS A 18 -1.895 -4.875 4.315 0.50 31.84 N
ATOM 158 CA BCYS A 18 -2.266 -5.806 3.263 0.50 31.60 C
ATOM 159 C BCYS A 18 -1.939 -7.242 3.717 0.50 31.75 C
ATOM 160 O BCYS A 18 -0.793 -7.566 4.049 0.50 31.65 O
ATOM 161 CB BCYS A 18 -1.558 -5.390 1.964 0.50 31.85 C
ATOM 162 SG BCYS A 18 -1.483 -6.547 0.602 0.50 31.63 S
...
ATOM 203 N ACYS A 22 -2.638 -8.291 -3.295 0.50 26.09 N
ATOM 204 CA ACYS A 22 -3.558 -7.246 -3.764 0.50 26.81 C
ATOM 205 C ACYS A 22 -3.259 -6.775 -5.187 0.50 27.42 C
ATOM 206 O ACYS A 22 -2.184 -6.285 -5.483 0.50 27.81 O
ATOM 207 CB ACYS A 22 -3.657 -6.044 -2.812 0.50 26.52 C
ATOM 208 SG ACYS A 22 -5.037 -4.895 -3.261 0.50 26.48 S
ATOM 209 N BCYS A 22 -2.501 -8.194 -3.113 0.50 28.39 N
ATOM 210 CA BCYS A 22 -3.228 -6.937 -3.282 0.50 28.74 C
ATOM 211 C BCYS A 22 -2.887 -6.357 -4.671 0.50 28.88 C
ATOM 212 O BCYS A 22 -1.949 -5.574 -4.813 0.50 29.38 O
ATOM 213 CB BCYS A 22 -2.893 -5.935 -2.147 0.50 28.91 C
ATOM 214 SG BCYS A 22 -3.281 -6.419 -0.381 0.50 29.70 S
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