This is the a second round of Reconstruction Puzzle 106. In that puzzle, we didn't provide any background information. The results of that puzzle were a definite improvement over the original structure, but there are some specific errors that we'd like to see if you can also improve too. Specifically, have a look at segment ranges 142-151, 182-196, 260-274, and 389-397 using the original PDB numbering. We think in those regions there might be what's called register shifts. Register shifts can happen in relatively low resolution structures, where the entire backbone gets shifted. We'd like to see what Foldit players can do to identify and perhaps correct them. Previous solutions should be loadable into this puzzle.
This is one where you may need to decode the instructions. For example, one range is listed as 142 to 151 "using the original PDB numbering". Using the segment info window, segments 114 to 123 show PDB# A 142 to A 151, meaning chain A, residues 142-151.
A quick tour with the segment info window shows that the whole thing may have started as a single chain, chain A. There are some big gaps. The current AA Edit and the like show multiple chains due to the gaps.
A more complete map of PDB to Foldit is in the works.
P.S., you can also load results from the previous round, Puzzle 2567.
PDB 5LAD is a match for the Foldit protein. There are a number of "missing residues" in the 5LAD experiment, but the original protein was all one chain.
For the suspected register shift areas, here are the start and end of each range in PDB and Foldit (FI) terms. The "sequence" field lists the amino acids involved.
#
PDB beg
PDB end
FI beg
FI end
sequence
1
142
151
114
123
ryeakvllvs
2
182
196
149
163
idggdlvilvvpidl
3
260
274
227
241
dvelttfsivesryr
4
389
397
350
358
hgvldrairp
The offset between the PDB residue and the Foldit segment is not constant due to missing residues. There are missing residues at the beginning, but there are also two gaps in the middle.
