![]() A symmetry operation represents a mathematical transformation that, when applied to the coordinates of one molecule, will transform it to its symmetry-related mate in the crystal lattice. Within this lattice, all molecules are ordered and related to each other by crystallographic symmetry operations of the symmetry group of that crystal (the possible symmetry groups are listed in a book called International Tables for Crystallography). Why is it an asymmetric unit? When the molecules are crystallized, they are arranged in the space lattices of the crystal. This means that a monomer within a dimer, a trimer, or a tetramer, becomes an asymmetric unit of the crystal. When crystallized, the oligomer symmetry axis may become a crystallographic symmetry axis. Often the subunits in these quaternary structures in solution are related by some symmetry - for example, two-, three- or four-fold rotation. The functional biological unit (the quaternary structure) in solution may contain several subunits of the same protein, arranged as dimers, trimers, or larger-order oligomers, as discussed earlier. We also need to remember that PDB files contain the so-called asymmetric unit of the crystal. Below is an example from the PDBsum link page (for mobile view, please click here). PDB, PDBe, and PDBsum provide plenty of additional data, including links to other databases where more information can be found. It is also possible to refine the search using the options provided at the PDB site. PDBsum and PDBe (PDB Europe) usually give more narrowed search results. ![]() Generally, one gets many hits, some of which would be unrelated to the search. We need to type the name of the protein into the search window on the PDB site. Using the PDB, we can easily find the structure of the protein of interest and assess its quality. This may be a source of confusion when we try to fetch a structure from the PDB - which one to choose if there are many entries of the same protein? For our purposes, we also need to remember that not all structures in the PDB are created equal, and we need to identify the one with the best available quality (see discussion of structure quality). There are many entries of the same protein in the database - some are mutant variants, others may be complexes with ligands (substrate analogs, inhibitors, cofactors), complexes with other proteins, etc. With the increasing number of solved structures, the number of protein databases increased, and new tools for analyzing protein sequences and structures were rapidly developed.Īlthough the number of structures in the PDB is rapidly increasing, one should remember that far from all PDB entries are unique. Then came the era of structural genomics - large consortia were formed to develop new technologies for crystallization and solving large numbers of protein structures. Now a Windows PC or a Mac is all we need. In the middle of the 1980-ties, a proper graphics monitor with a computer, which was needed for model building and refinement, would cost around 100 k dollars, obviously unaffordable for personal use for people interested in science. Cheaper computers also meant new software, which became much more user-friendly. The third factor, I believe, was the introduction of low-cost personal computers with ever-increasing computational and graphics processing power. In the early days of crystallography, we needed to optimize the crystallization conditions to grow crystals large enough for the relatively low-intensity laboratory X-ray sources. In addition, synchrotrons reduced the time required for the optimization of crystallization conditions. Several synchrotrons worldwide currently provide high intensity X-rays for quality X-ray data collection. Another essential factor was the introduction of synchrotron radiation for X-ray data collection. Cloning solved the problem proteins could be expressed in large quantities and purified for crystallization. Therefore, obtaining a few milligrams of protein for crystallization required large cell volumes. Before the cloning era, proteins were purified directly from cells, which substantially limited availability − there is always a limited number of copies of a particular protein in a cell. One of them was that cloning techniques started to enter the lab, and the number of different proteins and their quantity available for crystallization increased drastically. There are, of course, several reasons for the structural revolution.
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