Question: Crystal structure of lambda phage?
0
gravatar for DanielC
5 weeks ago by
DanielC100
Canada
DanielC100 wrote:

Dear Friends,

Can you please let me know if there is crystal structure available for "Lambda phage"? I would really appreciate if you could let me know the PDB of it. Thank you for your time.

e-coli phage lambda • 127 views
ADD COMMENTlink written 5 weeks ago by DanielC100

Did you try searching the PDB database?

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Sej Modha4.5k

Thanks! Yes, I did, there are quite a few, but I am not sure which structure is the one of Lamda phage for E-Coli. Do you have any idea if there is one? Thanks!

ADD REPLYlink written 5 weeks ago by DanielC100

There won't be a single crystal structure for an entire phage. What is it you need exactly? The phage structure overall, or the specific atomic structure of parts of it?

Lambda has been studied for a long time, so there will be lots of structures in all sorts of different conformations and co-crystallised with various other molecules, so you need to pick the one thats makes sense or is most useful to you.

ADD REPLYlink written 5 weeks ago by Joe14k

Thanks! I am looking for the tail fiber structure of the lambda phage. Could you please let me know about your suggestions on this?

ADD REPLYlink written 5 weeks ago by DanielC100

Do you have the sequence?

ADD REPLYlink written 5 weeks ago by Joe14k

No, i will see if lambda phage sequence can be found, any idea on this? once we have the sequence we do blast against pdb database; is this what you mean?Thanks

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by DanielC100
1

I would suggest you search the sequence using PDBs search tool: https://www.rcsb.org/#Subcategory-search_sequences

We cannot tell you definitively which crystal structure is the one you need, as it depends, as I explained above, about what conformations you care about, what analysis you intend to do, what cofactors you may or may not want etc.

A good first pass would be to find the sequence you know you're interested in, and start from the closest or longest match (since some residues will be missing in the structure almost certainly).

ADD REPLYlink written 5 weeks ago by Joe14k

It does not seem to me that you are showing much personal initiative to figure this out. Go to http://www.rcsb.org and enter "tail fiber lambda phage". At that point you will get bunch of hits, and need to go through them to find what specifically interests you. I am sure our ability to read is no better than yours, and this will not get done faster by you telling us what you want and us pointing you to a particular structure. It will be more efficient if you simply go through search results yourself.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Mensur Dlakic2.1k
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