[chimerax-users] .pdb from Protein Data Bank has more chains than expected

[Dr. Kevin M Jude]

Hi Phil, the pdb file represents the asymmetric unit of the crystal, the smallest unit that can be propagated by  the crystal symmetry operators to regenerate the crystal lattice. It is common for proteins to crystallize in a form that also contains noncrystallographic symmetry, ie symmetry operations that can’t be propagated through the crystal lattice. Sometimes this is biologically significant, eg in the case of a homoassembly, but other times it is simply the lowest energy way to fill a lattice. In such a case, multiple copies of the protein must be modeled to fill the asymmetric unit. Usually the copies are identical, or nearly so.

In chimeraX, you can select copies of chains you aren’t interested in and either hide or delete them.

Best wishes
Kevin

From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Date: Wednesday, November 9, 2022 at 4:47 PM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] .pdb from Protein Data Bank has more chains than expected
Hi Everyone,

I downloaded the 7FDL .pdb from the Protein Data Bank.  I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L).  I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein.  It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment.

Two questions.  Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B.

I have attached the .pdb file.

Thanks for any advise.

Phil McClean


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