hi,
I have a dimer protein with missing residues in both subunits.
I have the target sequence, the original protein pdb with missing gaps * (a.pdb* resolution 3.58 Xray structure)and another pdb of the same protein with missing residues included (*b.pdb* resolution 3.5 electron diffraction)
So i have to add missing residues with b.pdb as the template and rest of the protein exact to a.pdb)
In the given example:
>P1;1qg8structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG*
Here what extra alignment should be added if i have a pdb(*b.pdb*) with missing residues included which can be used as a template(same sequence).
Also can i add missing residues in both A and B units simultaneously.
Thanking you
On 5/3/12 3:29 AM, Mary Varughese wrote: > I have a dimer protein with missing residues in both subunits. > > I have the target sequence, the original protein pdb with missing gaps > *(a.pdb* resolution 3.58 Xray structure)and another pdb of the same > protein with missing residues included (*b.pdb* resolution 3.5 electron > diffraction) > > So i have to add missing residues with b.pdb as the template and rest of > the protein exact to a.pdb)
Yes, that should be fairly straightforward - simply use both templates in modeling, and align the model with a.pdb or b.pdb accordingly. If possible, try to overlap the regions a little so that Modeller can figure out the conformation of the missing regions.
> Also can i add missing residues in both A and B units simultaneously.
Sure, that's no problem. Your alignment might look something like:
>P1;a ... AAAAAAAAAA------AAAAAAAAAA/AAAAAAAAAA------AAAAAAAAAA* >P1;b ... --------BBBBBBBBBB--------/--------BBBBBBBBBB--------* >P1;model ... MMMMMMMMMMMMMMMMMMMMMMMMMM/MMMMMMMMMMMMMMMMMMMMMMMMMM*
(This assumes that you've edited b.pdb to only include the regions in the alignment above.)
Ben Webb, Modeller Caretaker
Sir,
Did you mean that i should edit the template(for missing residues) pdb so that it contains the co-ordinates of the missing residues only. ; and the alignment look likes ---------------------mmmmmmmm-------------------* where m stands for missing residues.?
But what you mean by overlap the regions a little so that modeller can figure out the conformation of the missing regions?
Thank you very much for your reply
On Thu, May 3, 2012 at 3:59 PM, Mary Varughese maryvj1985@gmail.com wrote:
> hi, > > I have a dimer protein with missing residues in both subunits. > > I have the target sequence, the original protein pdb with missing gaps * > (a.pdb* resolution 3.58 Xray structure)and another pdb of the same > protein with missing residues included (*b.pdb* resolution 3.5 electron > diffraction) > > So i have to add missing residues with b.pdb as the template and rest of > the protein exact to a.pdb) > > In the given example: > > > >P1;1qg8structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG* > > Here what extra alignment should be added if i have a pdb(*b.pdb*) with > missing residues included which can be used as a template(same sequence). > > Also can i add missing residues in both A and B units simultaneously. > > Thanking you > -- > Mary Varughese > Research Scholar > School of Pure and Applied Physics > Mahatma Gandhi University > India > >
On 5/4/12 12:22 AM, Mary Varughese wrote: > Did you mean that i should edit the template(for missing residues) pdb > so that it contains the co-ordinates of the missing residues only.
Yes (plus a few extra either side of the insertion). Since the alignment file must match the sequence in the *entire* PDB file, either you need to include the unused PDB sequence in the alignment (just misalign it so Modeller doesn't use it in the model - see FAQ #2) which can be a little awkward, or modify the PDB to remove the unused residues.
> But what you mean by overlap the regions a little so that modeller can > figure out the conformation of the missing regions?
If you look at the alignment in my previous email, you'll see that the model is aligned with both A and B for two residues on each side of each insertion. If you don't do that, Modeller won't know how to connect the missing regions with the rest of the protein.
Ben Webb, Modeller Caretaker
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Mary Varughese -
Modeller Caretaker