Element 2

In this element we will look at several nitty gritty validation details.
After finishing this element you will understand about five percent of the WHAT_CHECK error messages that deal with small details.

Threonine nomenclature problems

Get the WHAT_CHECK report for 1BFX from the FILES listed under the Miscellaneous heading. Go to the nomenclature section.

Question 13: What is written about Threonines in the nomenclature section of the 1BFX report? What does that actually mean? Do you agree that this is actually a chirality problem and not a nomenclature problem?

Answer

Question 14: Now look at the B-factor plot in the 1BFX report. Can you think of a reason why it is missing?

Answer

Now look up the 1BFX PDB file with MRS (the pointer to MRS is in the Pointers section).

Question 15: Read the header of the PDB file. Can you read from the header why there is no B-factor plot in the WHAT_CHECK report? And can you explain from the header how the Threonine-93 got ists Cγ and Oγ swapped?

Answer

Loops

Figure 45. The loop around Glu 169. Glu? I see no Glu. Indeed. What's going on?

Question 16: Load 1A1A.pdb (that file can be found under the exercise files) in YASARA. Find Glu 169 in the B chain. Which two problems do you see?

Answer

Question 17: The logical next question is why?

Answer

And now to see where we can go in the (very near) future... Work in pairs, one partner keeps the original 1A1A file open, and the other partner reads the PDB_REDO copy of 1A1A in in YASARA (this file is also present in the exercise files).

Discuss the differences.

Question 18: The authors of 1A1A deposited their reflections in 1997. Was that a good thing to do? Robbie made the PDB_REDO file. Why could Robbie produce better coordinates:
A) Because he is a better crystallographer
B) Because today we have better software, bigger computers, and more knowledge about the stereochemistry of proteins?

Answer

Water

Figure 46. The situation in 5TLN around calcium-3. Dashed lines are hydrogen bonds. Red balls are warers. The yellow ball is calcium-3.

Take the file 5TLN from the exercise file list, and read it in in YASARA. This is a very old file, so we could find many little problems. Given the age and the resolution, this is a relatively good PDB file. Take a look in the WHAT_CHECK report (that is also listed in under the exercise files). In that report, go to the Bumps section.

Question 19: Which is the worst bump? Can you find it in YASARA? Discuss with the assistants how this could have happened.

Answer