Closed since over 2 years ago
Novice Overall Prediction Electron DensityThe structure of this protein has already been solved and published, but 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. This one has two copies of the protein chain in the puzzle.
The only dimeric hit from blastp is PDB 5EO3, https://www.rcsb.org/structure/5EO3. 5EO3 has some unmodelled residues on PDB A,B 320,321 (numbers from pressing tab on a residue). I'm not really sure the puzzle treating them as completely absent is a good idea here..
Depends on purpose i think.
Generally crystallographers would either leave a gap between if the residue is competely disordered (instead of linking adjacent residues) or if the backbone is somehow resolved model it as alanine.
Because if it's not there at all and you force it in the map it can lead to a kind of bias and poor model correlation.
Since there's a big blob of green maps there (unmodelled densities) when contoured at 3 sigma which overlap the backbone (blue map typically contoured at 1 sigma, green and red 3 sigma) maybe better add it back. If have time maybe can put it back and recalculate the map to see if there's any red maps there, if no it should be there.
But I guess even if there's no green map, if you model it there first for a better fitting of other residues, and remove them before recalculation of the map maybe it can be useful, I am not sure. I'm still new to x-ray structure solution.
For computational chemists usually we need to manually add back these residues before we do simulation or virtual screening (if the missing region is within the targeted site). Still really depends on purpose.
(Edit: fix typos)
This puzzle was puckered due to missing residues.
The recipe Pucker Picker 3.0 RC 1 detected these puckers:
Pucker Picker 3.0 RC1 2341: Electron Density Reconstruction 53 2 puckers found! pucker 1 (ideality), segments 49-50 (protein), distance = 5.589, ideality = -1721.693, -1723.598 pucker 2 (ideality), segments 150-151 (protein), distance = 7.741, ideality = -7825.07, -7827.094
