Placeholder image of a protein
Icon representing a puzzle

2155: 588-residue Electron Density Reconstruction 8

Closed since 4 months ago

Advanced

Summary


Created
June 01, 2022
Expires
Max points
100
Description

Note: Due to a bug in cutpoint behavior, this puzzle was closed early land reposted as Puzzle 2155b. Players may save solutions from this puzzle and load them into the reposted puzzle.



That is not a typo, this Electron Density puzzle has 588 residues! This will require using the new Trim Tool!



You'll also want to use the Radius Slider in the Electron Density panel, to view only density within a ball of the given radius. Remember that you select a sphere of residues with CTRL+SHIFT+click and drag, as demonstrated on the recent Lab Report! (Just make sure to click and drag on the protein, and not on the background.)

Top groups


  1. Avatar for Marvin's bunch 100 pts. 53,072
  2. Avatar for Go Science 2. Go Science 52 pts. 51,697
  3. Avatar for Void Crushers 3. Void Crushers 24 pts. 49,031
  4. Avatar for Contenders 4. Contenders 10 pts. 47,488
  5. Avatar for Anthropic Dreams 5. Anthropic Dreams 4 pts. 47,439
  6. Avatar for L'Alliance Francophone 6. L'Alliance Francophone 1 pt. 42,161
  7. Avatar for Australia 7. Australia 1 pt. 19,574
  8. Avatar for Gargleblasters 8. Gargleblasters 1 pt. 0
  9. Avatar for Foldit Staff 9. Foldit Staff 1 pt. 0

  1. Avatar for dcrwheeler
    1. dcrwheeler Lv 1
    100 pts. 53,179
  2. Avatar for jausmh 2. jausmh Lv 1 88 pts. 53,072
  3. Avatar for ichwilldiesennamen 3. ichwilldiesennamen Lv 1 77 pts. 51,697
  4. Avatar for Trajan464 4. Trajan464 Lv 1 67 pts. 51,226
  5. Avatar for ZeroLeak7 5. ZeroLeak7 Lv 1 58 pts. 50,405
  6. Avatar for NinjaGreg 6. NinjaGreg Lv 1 50 pts. 50,397
  7. Avatar for toshiue 7. toshiue Lv 1 43 pts. 49,822
  8. Avatar for Sandrix72 8. Sandrix72 Lv 1 37 pts. 49,612
  9. Avatar for Anfinsen_slept_here 9. Anfinsen_slept_here Lv 1 31 pts. 49,044
  10. Avatar for Simek 10. Simek Lv 1 26 pts. 49,031

Comments


LociOiling Lv 1

The protein in this puzzle matches PDB 5DJW, as shown below in the Jpred alignment results.

The Foldit protein has a couple of gaps in its sequence. In the puzzle, these gaps are marked by light blue connectors that look a little like cutpoints. I'm calling them "uncut points". Unlike a cutpoint, they can't be closed, and don't affect whether the score is valid.

If you look at the details for 5DJW, the gaps correspond to "missing residues", which were part of the sequence, but then weren't found in the electron density results.

Assuming the crystallographers were close to begin with, the segments on either side of the uncut points should stay near where they start. Left to their own devices, the uncut points seem to want to close up, much like cutpoints.

>5djw_A mol:protein length:697  Alpha-glucosidase II
          Length = 697

 Score = 1213 bits (3139), Expect = 0.0
 Identities = 588/612 (96%), Positives = 588/612 (96%), Gaps = 24/612 (3%)

Query: 1   SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW 60
           SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW
Sbjct: 46  SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW 105

Query: 61  MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT 120
           MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT
Sbjct: 106 MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT 165

Query: 121 GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP 180
           GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP
Sbjct: 166 GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP 225

Query: 181 KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW 240
           KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW
Sbjct: 226 KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW 285

Query: 241 PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPED------- 293
           PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPED       
Sbjct: 286 PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPEDNLHRGGG 345

Query: 294 ---------YHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC 344
                    YHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC
Sbjct: 346 KLPAGTHLQYHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC 405

Query: 345 WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN 404
           WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN
Sbjct: 406 WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN 465

Query: 405 NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE 464
           NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE
Sbjct: 466 NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE 525

Query: 465 EEAFLVGDNLLIIPAFANQPALPKGIWKEL--------DKYQAKMKIRGGAIIPTGKIIQ 516
           EEAFLVGDNLLIIPAFANQPALPKGIWKEL        DKYQAKMKIRGGAIIPTGKIIQ
Sbjct: 526 EEAFLVGDNLLIIPAFANQPALPKGIWKELSLVEGDQNDKYQAKMKIRGGAIIPTGKIIQ 585

Query: 517 NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT 576
           NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT
Sbjct: 586 NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT 645

Query: 577 KKTGKYNTENKD 588
           KKTGKYNTENKD
Sbjct: 646 KKTGKYNTENKD 657

bkoep Staff Lv 1

Thanks for the feedback LociOiling! The starting cutpoints should not close up on their own… that seems like a bug. We'll try reposting the puzzle with a correction.