I am working on a protein from Leishmania donovani DD8 strain but according to gebeDB genome sequence of Leishmania donovani BPK282A1 strain was available.
If we have crystallized the protein from DD8 strain:
1.PDB will accept those type of structures or not?
2.(If) Is there any guideline to depositing structures from unsequenced organism?
Please provide your suggestions.
1. Yes. The PDB does not require deposited structures to originate from sequenced genomes. You can even deposite proteins with artificial primary structures (originating in no organism, or if you like, in the organism formed by transforming an expression strain with recombinant DNA.)
2. Just deposit it like usual. If there's a field that doesn't make sense, consult with the PDB deposition staff. They're available to help.
Ryan is right, there's no problem in depositing the structure, we have lots of structures with no sequence DB reference. PDB deposition staff are a very friendly lot (even me!)
Crystallography is also a way to obtain/correct sequence information. Especially those sequences that were deposited long time ago can be inaccurate.
Look at it the other way round: the sequence that can be derived from your structure will be available to the public soon!
I don't see a big problem. PDB will accept it with warnings. But, most importantly, the resolution of your crystal structure makes the difference. A sequence guessed from a high resolution structure (say < 2.0 Angstroem ; you must check visually your electron density, residue by residue, and act accordingly), supported by comparison with the sequence of the same protein from a cosely related strain, is likely to >> 95% correct.
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