Why is ASP on PDB 3NIR with pH 7 not deprotonated?

07 July 2014 5 6K Report

If I open with Jmol and select model A or C, both have hydrogen bonding with the oxygen. Should this hydrogen being there?

From the 3NIR document this is the method used

60% ethanol in water, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

thanks

Lionel Nauton

hello,

certainly not, the problem here is the very high resolution (0.48 A), and automatic building, all proton are added very strangely, it seems that after adding H automatically , a minimization was performed and H were dispersed because lot of them are too close, and if you look attentively, the two chain are not well named, so it explain the result of the minimization.

for the ASP, if the pH are 7 as explain, this position is near the solvent, and there is no specific interaction with closed residues for explian a specific local pH, so it was not protonated.

and if look for GLU it's the same things.

all structure factor are available, i think , it could be interesting to redo the refinement with phenix, or refmac has you prefer, and cut the resolution to 1.6 A, it could help to put automatically H. And if you look for Rfree in PDB site, you don't find it, there probably a mistake with refinement....

it's a joke, how this PDB could be deposed, in the DATA BANK, the refinement is not complete. some résidues are missing, when someone else are refined in two or three position,

be carrefull, the paper seems to be a methodologic X-ray paper, so they probably want to show specific things in relation with high-energy source so

i confirmed that you need to redo refinement.

Thiago Benazzi Maia

Hello Lionel.

Thanks a lot for checking the PDB file so careful. I'll follow your suggestion and do the refinement with the software you suggested. I see now that I have to be careful with the pdb files from this website.

thanks and best regards

Thiago Benazzi Maia

In case somebody else is having the same question this is a document talking about mistakes in the databank.

http://journals.iucr.org/m/issues/2014/03/00/dc5002/dc5002.pdf

And pdb files can be checked from here.

http://www.cmbi.ru.nl/pdb_redo

Lionel Nauton

hope this help...3NIR refine with phenix... at 0.57 A ,

Thiago Benazzi Maia

Now, finally I can use that pdb, thanks a lot for doing that. I tried to download phenix but its only for registered universities so I started to learn refmac.

thanks a lot

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