Dear all,
I wonder why I can only see one chain on PDB website and see 2 identical chains in PDB file that I downloaded(opened with PyMol). I checked the sequence as well as ligands/ ions attached, they were really identical. Could anyone please help me with it...did I do anything wrong? Or is it normal and I should extract only one chain in PyMol?
Hello.
Probably, your protein exists as a dimer in its native state. That's why you have two identical chains. You can extract one and proceed for further docking or simulation with ligands.
In a crystal structure you have the asymmetric unit. This is the basic building block of the crystal. You can have a dimer in this unit, and symmetry operations to connect, by rotating the asymmetric unit d degrees and translating by n distance. This symmetry propagates over and over again in the crystal.
Basically, crystals are full of symmetry and proteins crystallize at very high concentration at least 10 mg/mL typically. So the proteins are very tightly packed and sometimes packed as dimers or trimers. The packing of the proteins doesn't necessarily mean the protein is natively an oligomer. That is just how symmetry works in a crystal. But sometimes the protein is actually an oligomer in solution. This makes sense for a helicase which are hexamers in solution. They wrap around DNA like a ring.
Note: If you look at the crystal structures of lysozyme, you will probably find monomers, dimers, trimers, tetramers, and hexamers. That's the beauty of unique crystallization conditions. There are hundreds of crystallization conditions for lysozyme. Now which one is it really?
Adron Ung Thank you for the detailed explanation! After checking the paper attached to my PDB, I found, yes, it‘s a P-L complex which shouldn’t be a dimer. I know nothing about the wet-lab part, my lecturer smeared through the crystallization process. Anyway thank you very much!
Tini Chu , no problem crystallization is a complicated process. It is hard to understand it even as a crystallographer. No program can predict the crystallization conditions of a protein (concentration, pH, temperature, viscosity, time, and cryoprotection conditions). Crystallization is totally empirical. Proteins crystallize when they are happy.
Thankful. Honestly, I am learning how to be an enzymologist and it is like a switch flipped in my mind when I figured out that I do not need a structure to know how an enzyme works. There are a lot of things one can learn about an enzyme in a wet lab without even a structure.
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