This is my first post on ccp4bb, and I am seeking advice on a problem I have
My crystal structure revealed a nickel ion chelated by 4 nitrogen atoms: 3
from protein chain A and 1 from chain B. A and B form dimers. The nickel
was placed in the same asymmetric unit as chain A, and it is linked to the
chain B from a different asymmetric unit.
The space group is P21 21 21, and from coot, it shows that the symmetry
operation required to bring chain B in contact with the nickel ion of its
asymmetric unit is:
[X+1/2, -Y+1/2, -Z + (0 0 1)]
According to http://www.genome.ad.jp/dbget-bin/www_bget?pdb+1UBQ (at REMARK
290) and from my understanding, this corresponds to the code 4556 (from 4555
+ the 001 translation).
Based on http://www.wwpdb.org/documentation/format23/sect6.html, I believed
I could specify this link by including the following into my pdb file:
LINK NI NI M 1 NE2 HIS B 103 1555 4556
However, when I run Refmac5 of ccp4i6.0.2, this line appears to be
completely ignored by the program. On the other hand, the 3 contacts
between Ni and chain A were all detected and refined with no problems, as
the previous cycles of refinement have generated such a line in the pdb file:
LINKR N HIS A 2 NI NI M 1 HIS-NI
Under "Setup Geometric Restraints" in Refmac5, I have attempted to
check/uncheck the "Links between symmetry related atoms" option, and tested
it in combination with All others if "defined in file only and/or residues
So far, I have no luck in getting Refmac5 to recognize this bond. Are there
obvious things that I may have missed? Or did I do something completely wrong.
Any comments/suggestions would be greatly appreciated.