[ccp4bb] Model submission
Dear All, I'm working out the finer details on a structural paper for submission to JBC. I'm having a slight problem with how to present my data. I've got a high resolution (1.46 A) truncated structure of the protein with the N-terminal 38aa removed. I've also got data from lower resolution (2.68 A) crystals of the full length protein. There's no significant difference between the high res and low res proteins in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there is broken density for the first 38aa from the full length data it's too poor to model into. I want to present a figure which shows the density corresponding to the first 38aa and where that fits with the rest if protein molecule. What I'm unsure of it whether I will be required by the journal to submit a model from the lower resolution data to the PDB in order to present this figure. Bearing in mind the density doesn't allow any additional residues to be modelled compared to the high res. structure. Your opinions or advice on how best to present this data would be welcomed. Cheers, Rhys
Re: [ccp4bb] Model submission
What extra insight does the full-length protein give, i.e., why not just chuck it? JPK On Tue, Jun 19, 2012 at 10:35 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: Dear All, I'm working out the finer details on a structural paper for submission to JBC. I'm having a slight problem with how to present my data. I've got a high resolution (1.46 A) truncated structure of the protein with the N-terminal 38aa removed. I've also got data from lower resolution (2.68 A) crystals of the full length protein. There's no significant difference between the high res and low res proteins in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there is broken density for the first 38aa from the full length data it's too poor to model into. I want to present a figure which shows the density corresponding to the first 38aa and where that fits with the rest if protein molecule. What I'm unsure of it whether I will be required by the journal to submit a model from the lower resolution data to the PDB in order to present this figure. Bearing in mind the density doesn't allow any additional residues to be modelled compared to the high res. structure. Your opinions or advice on how best to present this data would be welcomed. Cheers, Rhys -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Model submission
On Tue, Jun 19, 2012 at 8:35 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: There's no significant difference between the high res and low res proteins in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there is broken density for the first 38aa from the full length data it's too poor to model into. I want to present a figure which shows the density corresponding to the first 38aa and where that fits with the rest if protein molecule. What I'm unsure of it whether I will be required by the journal to submit a model from the lower resolution data to the PDB in order to present this figure. Bearing in mind the density doesn't allow any additional residues to be modelled compared to the high res. structure. This may be true today, but there is no guarantee that it will still be the case in five years, or ten, or however long it takes for the software to improve. I'd argue that anything you illustrate in the paper should end up in the PDB anyway, but if there is any chance that someone could improve on your structure in the future and possibly learn something new as a result, it's worth depositing for that reason as well. Otherwise the data will probably be lost, and we'll never know if those extra residues could have been modeled. (Although I suspect that it would be more helpful if the images were also available, instead of having to start from the processed data.) -Nat
Re: [ccp4bb] Model submission
On Tue, 2012-06-19 at 11:07 -0500, Jacob Keller wrote: What extra insight does the full-length protein give, i.e., why not just chuck it? It proves that the N-terminus does not have a strong influence on the rest of the structure. Other words, it's OK to draw conclusions about the full-length protein from truncated form. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Model submission
I echo with Nat and support depositing both structures. Despite the fact that the 38 residues are disordered, these are 2 different proteins (chemically). The disordered residues may not lead to a better model, but they do carry information. They are there and still take up physical space, thus they may change the crystal packing. Regardless of journal requirement, i think it is good practice, and nothing to lose, to deposit both. Yu Wai Chen On 19 Jun 2012, at 18:57, Nat Echols nathaniel.ech...@gmail.com wrote: On Tue, Jun 19, 2012 at 8:35 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: There's no significant difference between the high res and low res proteins in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there is broken density for the first 38aa from the full length data it's too poor to model into. I want to present a figure which shows the density corresponding to the first 38aa and where that fits with the rest if protein molecule. What I'm unsure of it whether I will be required by the journal to submit a model from the lower resolution data to the PDB in order to present this figure. Bearing in mind the density doesn't allow any additional residues to be modelled compared to the high res. structure. This may be true today, but there is no guarantee that it will still be the case in five years, or ten, or however long it takes for the software to improve. I'd argue that anything you illustrate in the paper should end up in the PDB anyway, but if there is any chance that someone could improve on your structure in the future and possibly learn something new as a result, it's worth depositing for that reason as well. Otherwise the data will probably be lost, and we'll never know if those extra residues could have been modeled. (Although I suspect that it would be more helpful if the images were also available, instead of having to start from the processed data.) -Nat
