We will now look where you can find quality-related information, electron-density maps, etc. for any structure that has been archived in the PDB. We will use the resources available from PDBe, but you may find (some of) the information and similar tools also at other sites such as PDBj, RCSB PDB, PDBsum and PDBREPORT. To begin with, we shall use PDB entry 1CBS as an example: https://pdbe.org/1cbs
Information on the entry page
Go to the entry page for entry 1CBS. There are a number of places where you can find information about the quality of the structure:
Near the top of the page, you will find information about the experimental method(s) used to determine the structure. In the case of diffraction and (sometimes) cryo-EM structures, the resolution will also be shown. Below this are the release date and two summary sliders, one for the overall quality of the model and one for the overall fit of model and data (if no data was deposited, this will be replaced by a grey bar).
In the menu on the right, there are three relevant options: View, Downloads and 3D Visualisation. View and Downloads are very similar - they allow you (amongst other things) to view or download the wwPDB validation report for this entry. Selecting the 3D Visualisation option brings up the LiteMol viewer (there is a quick guide that shows you how to use and interact with LiteMol):
Play around with the menus and mouse controls and see if you can reproduce the following display (hint: left-mouse rotates, middle-mouse changes the slab, and right-mouse zooms in/out):
Further down on the page, you will see a panel called "Experiment & Validation":
The link to Details will take you to a separate page with, surprise!, more details related to validation and refinement.
Download the validation report for this entry. Typical questions that you can often answer after a cursory look at such a report include:
- What is your impression of the quality of this entry?
- How does it compare to other entries in the PDB and to other crystal structures at similar resolution?
- Are there any residues with a poor fit to the density?
- Are there any consecutive stretches of residues with many outliers?
- Is the geometry of the ligand in order?
- Does it appear to fit the density well?
Q.12. What are your answers to the above questions for 1CBS, based on the validation report?
Q. 13. What are the values of Rfree and of (Rfree - R) for 1CBS? Are these good or bad?
Inspecting the macromolecule
Locate the link to Molecule details and follow it:
You will now come to a page that contains coupled sequence, topology and 3D structure viewers. Mouse-over on a residue in the sequence viewer and it will be highlighted in the two other displays. Click on a residue and the 3D viewer will centre on that residue. The residue quality is displayed in the sequence viewer and you can colour both the topology plot and the 3D model by residue quality. You can also switch the electron-density maps on in the 3D viewer if you like (e.g., by simply clicking on an atom). Try to reproduce the following display:
Inspect some of the residues that are not green in the quality plot and assess how well they are defined in the electron density. What do the small triangles above the PDB sequence signify?
Inspecting the ligand
Go back to the entry page and click on the chemical structure of the ligand. It is called "REA", but what is its proper name (actually, it has many different names - one will do)?
You will now be taken to a page with more details about the ligand, its interactions and its density (if available):
Q. 14. Are the interactions between the protein in 1CBS and its ligand "sensible"?
Q. 15. How good is the electron density for the ligand in 1CBS, compared to that of the protein?
Q. 16. It has been suggested (reference) that residues 20, 29 and 30 change their sidechain conformations upon ligand-binding to form a non-sequential/spatial Nuclear Localisation Signal. Inspect the density for these three residues in both the apo structure (1XCA) and the holo structure (1CBS). Are the changes in conformation supported by the data (density)?
