Using this tutorial:
 This website runs the Jmol molecule viewer. You will need a Java-enabled browser to view this website. Refresh your browser to resize applet to your screen size.

You can follow the tutorial below while watching short animated scripts by clicking the appropriate buttons.  At anytime, if you want to change the view of the structure, do the following:
Rotate: Click on mouse and drag
Zoom: Scroll wheel on your mouse or +Shift and left click
Move: +Ctrl and right click

If you are familiar with RasMol commands, you can also use them through the JMol console.

Default view with linker
Backbone 350, sidechains wireframe 300

Protein backbone:

Residues 2-122 colored blue (Regulatory domain)
  90-122 within this region in light blue (interface with effector domain)

Residues 123-128 colored grey (Linker)

Residues 129-228 colored pale green (Effector domain)
Residues 191-206 dark green (DNA recognition helix)

Sidechains:

Residues 56, 83, 102 (Switch residues) have backbone colored green and sidechains in CPK

Residues 190 (interacts with residue 102 in inactive form), 98, 200, 183, 119, 76, 155 also have sidechains displayed

Remove linker
Residues 123-128 will be missing from the model and will be "filled in" using flexible tubing

Tutorial and scripts prepared by Stephanie Hanchuk and Andrew Young

PDB File: 2GWR

Friedland, N.,  Mack, T.R.,  Yu, M.,  Hung, L.W.,  Terwilliger, T.C.,  Waldo, G.S.,  Stock, A.M. (2007) Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 46: 6733-6743