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Electron Density maps : lysosyme

To complete this tutorial, you will need to download some material (coordinates and electron density map of the lysozyme).

The data set has kindly been made available by Dr. Doug Ohlendorf. Nate Winter did a rigid body refinement of the coordinates deposited by K.P. Wilson, B.A. Malcom and B.W.Matthews (pdb entry 1hel) to Doug Ohlendorf's data set.

material for this tutorial:
hel dn6 map (.zip 640 Kb)

The downloaded material contains 5 files: the electron desity map (1hel.dn6), coordinates of two slightly different models of lysozyme (1hel.pdb and 1hew.pdb), a readme, and a model of lysozyme in which four residues have been replaced with ALA (mutant.pdb).

In this exercise, you will use the map to identify the correct amino acid in each case replace ALA with it, and fit it into the map.

 

edm2

Stereo detail of a part of the lysozyme contoured at 2.0 sigma. Real-time rendering directly from Swiss-PdbViewer.

 

Step by Step

  • First of all, if you are using a Macintosh, make sure that Swiss-PdbViewer has at least 6000Kb of free memory to run (click on the icon, press Command I, and adjust the memory allocated to the program). Then launch it.
  • Open the file "1hel.pdb"
  • Then, verify that the checkbox "center upon loading" of the "General preference" is not checked. If it was checked, uncheck it, close the protein and reload it.
  • Center the view by hitting the "=" key of the numerical keypad (right mouse button on the PC), and enable the "Slab" item of the Display Menu.
  • Click on the first button at the top left of the main window and set the "slab depth" to 8Å in order to limit the quantity of information displayed on screen at the same time.
  • Select the Open DN6 Map from the file menu and load the file "1hel.dn6".

    A dialog will appear. The upper part provides some information about the unit cell size: the length along its axis, and the angle between the axis.

  • Choose the "Display around CB" radio button, set the value to 6, 6, and 6 and contour at 1.0 sigma.
  • Load the protein 1hew.pdb and make it active layer.
  • Colour it by RMS. Almost everything will appear dark blue, meaning that superposition is perfect. But one region is coloured more brightly.
  • Bring up the align window, select the zone coloured by option clicking (right mouse button on PC) and hit the return key to display only the selected residues.
  • Control click (Shift Control-Click for the PC) on the Pro70 residue of 1hel which will center its CA in the view. Inspect the region. The backbone is flipped. This region differs between the two pdb entries. Colour all by B-factor, and observe that once more this is a region with relatively high B-factor.
  • Close the protein 1hew.pdb, and redisplay every amino acid of the 1hel.pdb protein.
  • open the protein "mutant.pdb" As you can see, it is not superposed onto 1hel. In fact it should be but as you have previously rotated the protein to inspect it, the referential has changed. close the protein "mutant.pdb", use the item "reset orientation" of the edit menu and immediately reload the protein "mutant.pdb". Observe that the protein is now perfectly superposed.
    This illustrate the importance of the RESET orientation, that should be used whenever you save a modification into a protein (unless the "save in Original Orientation item of the File Menu is enabled, in which case it will be done automatically). Otherwise when you reload it, it will no longer fit into the electron density.
  • Hide the "1hel.pdb" layer by disabling the visible box of the control panel, and switch to the "mutant.pdb" layer.
  • Center the view on Ala 38 (as you did previously with Pro70). Note that a blob of electron density is not occupied by any atoms. Try to figure out which residue should be put at this location (without cheating by looking at the solved structure!). Click on the mutate tool in the main window, click on any atom of the Ala 38, and browse the rotamer library of your suspected residue (by hitting the * key of the numerical keyboard). Accept the mutation of the rotamer that fits more closely to the electron density. No rotamer fits perfectly, and you will have to tweak the torsion angles. Click on the torsion tool and hold down the key number 2 while clicking and moving the mouse. It will rotate the bound binding the CB and the CD atoms. Adjust at best the sidechain within the electron density (you might have to use also the "1" key to rotate around the CA-CB bond. Once you are satisfied, accept the torsion.
  • Repeat the process for residues 59, 64 and 66.

    Then make the "1hel.pdb" layer visible and compare your work with the solution.

Note: in real life, after having tweaked the residues, the atoms positions are refined again with X-PLOR, and a new inspection of the map and tweaking is done until everything seems to fit properly.