Lab 1: PROCEDURE Part 1
NOTE: Before lab, you are expected to read through the procedure instructions. You should be familiar with what you will be doing before lab starts.
NOTE: The instructions for this lab were written for a Mac. However, PyMOL is virtually identical on a PC, so we don’t anticipate any problems.
NOTE: The times in parentheses are approximate suggestions of how much time it should take to complete the tasks. Ideally, this lab can be completed in about three hours.
PART 1: GETTING FAMILIAR WITH PROTEIN STRUCTURE (45 min)
Explore the PDB site (5 min)
- Go to the PDB website (link opens in a new tab): Protein Data Bank
- In the search box at the top of the page you can type the name of any protein you like in the search box, or you can use the “PDB code”, a code of four alphanumeric characters that defines a structure. If you don’t know what to type try, for example, carbonic anhydrase.
- You will get a list of results. Click on one of them and you will find its description page, including the Primary Citation (the paper where the crystallography was presented), the Molecular Description (the name of the protein and its classification), and possible ligands.
- Under the picture you’ll find the Experimental Details, which include the resolution (<1.5 Å: very high; <2 Å high; <2.5 Å medium), space group (the geometry of the crystal), R-value and R-free (quality control numbers; generally these should be ~10% of the resolution or less).
- The PDB code (e.g. “3IEO”) is in the top-right corner.
- Try a number of searches for proteins that you have studied. Note down the PDB code to open them in PyMOL later.
Visualize proteins with PyMOL (15 min)
- Open PyMOL.
- Note the tool bar on top, the menus, and the command text box underneath them (next to the “PyMOL>”). (See figure 1.1). Typing a command in the command box can perform many of the functions.
- Type in the command “fetch <pdb code>” (e.g. “fetch 3IEO”). This will download the structure from the PDB web site and the protein will appear in the main portion of the screen.
- Using the mouse:
- Clicking on the background and moving the mouse will rotate the molecule around the X and Y axes (clicking at the edge of the screen will rotate around Z axis).
- Clicking on the molecule will select residues (or chains, or atoms, depending on the current mode).
- Right click will zoom in or out on the molecule (move mouse up and down).
- The middle button can be either clicked or rolled.
- Clicking the middle button will allow you to move the structure sideways (translation).
- Rolling the mouse wheel will slice away Z-planes (you’ll see only a slice of the protein), a good way to focus only on some details of the protein.
- Objects: In the right panel you will see two or more objects: all, one or more <pdb code>(i.e. 3IEO), and possibly some selections ‘(sele)’. You can click on these buttons to display or hide molecules without deleting them (light grey buttons are displayed, dark grey butto