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Electron Density maps : fatty acid binding protein

To complete this tutorial, you will need to download some material (coordinates and electron density map of the lysozyme). This data set has kindly been made available by Dr. Jim Thompson, Dr. Nate Winter and Prof. Len Banaszak

material for this tutorial:
fabp dn6 map (.zip 553 Kb)

 

edm

Stereo detail of a part of the fatty acid binding protein. Rendering with POV-Ray.

 

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 pdb file lfabp .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 "lfabp.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. Note that the axis are not necessarily orthogonal. It all depends on the crystal symmetry. In this case, there is an angle of 120° between axis x and y.

ucell

Below are some information on the number of sections available in the map. As a whole edm is pretty heavy to handle, it is advised to display only a subpart of it. In our case, we will display only from sections 50, 20 and 40 (along X,Y and Z respectively) to sections 80, 50 and 56.

The last part of the dialog let you decide what will be the cutoff density for the contouring, i.e. decide what are the limit between a dense zone and a zone with low edm.

Type 2.5 in the field and accept these settings. Amino-acids belonging to the antiparalell strand 99-113 are perfectly fitted within the electron density map. What you see is in fact the final stage of the process. During initial stages of the resolution of a protein, edm are much more messy. Hold down the shift key while clicking and moving the mouse toward you to move the slab toward you. Some new parts of the protein will be revealed, all of which are not contoured. Remember that only a subpart of the edm was selected to be displayed. Play a little with the protein; look at the anti parallel b-stands, and so on.

  • Now go to the control Panel and click on the Asp106 while holding down the control key (shift Control for PC). This will automatically center its alpha carbon in the view. Zoom in. Note that the sidechain is not buried into the edm. It means that the location of the carboxyl group is not very well defined in space. As a matter of fact, sidechains of surface residues tend to be more flexible and therefore do not diffract very well.
  • Go back to the edm preferences dialog, and enable the second contour with a 1.5 sigma value. Click on the dotted checkbox, and accept the settings. A second contour, englobing more parts of the structure, among those the CG of Asp106 appears with an other colour. By decreasing the sigma value, you contour parts of the map that have a smaller electron density than when you use a high value.
  • Go back to the same dialog by hitting command+Y (control+Y for the PC), disable the display of the second contour and enable the dotted checkbox of the first contour. The display will now look like a cloud of dots, and the amino-acids appear more clearly within the density (this mode will be useful until I add a Z-buffer and also maybe a color-distance fading feature).

    As you have noticed, only the part of the edm you have selected to be displayed are actually shown. If you want to inspect all amino-acids one by one to see how well they fit into the edm, it would be useful to display only subpart of the edm corresponding to the residue you currently closely inspecting. Well, this is possible.
  • Bring back the edm dialog and enable the radio button entitled "Display around CB". By default, only parts of the edm lying within 5Å of the carbon beta of the currently centred residue (Ion our case Asp106) will be displayed in each direction along the unit cell axis.
  • Center the view on the next residue (simply hit the right arrow key) and a new portion of the edm will be displayed. Navigate down along the peptide to look at the edm, and stop on the residue Asp87. Here again, you can see that only no density is displayed around the sidechain. It is therefore very useful to be able to change the sigma value used for the contouring. This can be done without using the edm preference dialog: simply hit the down arrow key and the sigma contouring value will be decreased by 0.1. Hit the down arrow key 10 times more and look how the edm displayed increasingly covers the atoms. (note: typing the down arrow key while maintaining the shift key down will decrease the sigma value for the second contouring value).
  • Colour the protein by B-factor. Look at how the sidechain of the Asp87 appears reddish. This means indeed that the electron density is badly defined in this area.
  • Now Bring back the edm dialog and enable the coarse contouring along the Z axis. The contouring will be less fine bet the display should appear slightly less cluttered and faster.Play a little with the coarse checkboxes to look at the effect. Usually, working with one or two axis coarsely contoured allows a good rendering speed without noticeably affecting the display precision.
  • Click on the small text icon located at the right of the earth icon. in the main window. The text file will the coordinates of the currently active pdb file are displayed. Scroll down to the residue Asp87, and look at the B-factor of atoms OD1 and OD2 (last column containing digits). It is 85.39 and 84.53, which is very high. Colouring a protein by B-factor allows to immediately identify regions that are more accurately fixed in space than other (usually the core of the protein).

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