2353: Electron Density Reconstruction 57 (with DNA!)

Closed since over 2 years ago

Summary

• Created: September 12, 2023
• Expires: September 21, 2023 at 18:00 UTC
• Max points: 100

Description

This puzzle is a bit different than previous Reconstruction puzzles. Like others, the structure of this protein has already been solved and published, and close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. The difference is that in addition to a protein in this puzzle, the protein is bound to DNA! So we're curious if Foldit players can improve both the protein and the DNA using the electron density. Not every tool that works well with proteins also works with DNA, so this might take a bit more time to figure out strategy.

• Sequence: Protein: MATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLAKQKK DNA: GTGATCGC

Top groups

• 1. Anthropic Dreams 100 pts. 24,858
• 2. Contenders 70 pts. 24,834
• 3. Go Science 47 pts. 24,829
• 4. L'Alliance Francophone 30 pts. 24,763
• 5. Marvin's bunch 19 pts. 24,655
• 6. FamilyBarmettler 11 pts. 24,325
• 7. Void Crushers 7 pts. 24,232
• 8. Belgium 4 pts. 23,997
• 9. Australia 2 pts. 23,923
• 10. Gargleblasters 1 pt. 23,917

Top soloists

• 11. Punzi Baker 3 54 pts. 24,686
• 12. fpc 51 pts. 24,655
• 13. Steven Pletsch 48 pts. 24,652
• 14. alcor29 45 pts. 24,621
• 15. blazegeek 42 pts. 24,603
• 16. georg137 39 pts. 24,537
• 17. Bletchley Park 36 pts. 24,531
• 18. Bruno Kestemont 34 pts. 24,528
• 19. BackBuffer 31 pts. 24,523
• 20. akaaka 29 pts. 24,522

Comments

[rosie4loop]

This is entry 1C8C from the RCSB PDB. Resolution is high, but the model quality can be improved.

Resolution of the ED is high so the density is quite clean. However there are some bugs when the game handling DNA. See https://fold.it/forum/bugs/puzzle-2353-ed-puzzle-issues-recipe-idealize-and-trim-tool for details.

Edit 1: I also posted a workaround of the issue here (https://fold.it/forum/posts/77102)
Edit 2: Add PDB link

[Artoria2e5]

PDB-REDO entry says that the rotamers are probably very bad; we can shake that out. The handful of rama issues are probably best idealized or remixed out. Clashes (bumps) are not too bad.

[rosie4loop]

For a high resolution structure like this, water densities are visible. Those perfect spherical densities in the map could be a water oxygen. Some of them are within hbond distance that could contribute to protein structure stability or DNA interaction.

Probably challenging at this stage for Foldit to handle this, though.

[rmoretti]

How best to handle waters in these electron density puzzles is something we're currently discussing. For best results, they need to get added back in. We may eventually implement tools to allow players to add/remove waters, but you're correct that it's challenging to get Foldit to handle waters properly. Right now I believe the approach is to add them back in with a post-processing step.