The RCSB PDB site (www.pdb.org) provides as sequence motif search as an advanced search option. For example to search for a N-terminal (His)6 tag, use the following regular expression:
^HHHHHH
or HHHHHH to find any sequence with a (His)6 pattern.
Click on this link to retrieve all sequences with a (His)6 pattern:
http://www.pdb.org/pdb/search/smart.do?smartSearchSubtype_0=MotifQuery&motif_0=HHHHHH
For more details about the sequence motif search are available at:
http://www.pdb.org/pdb/staticHelp.do?p=help/advancedsearch/sequenceMotif.html
Best regards,
Peter Rose
RCSB PDB
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Snijder, Arjan
Sent: Friday, January 07, 2011 6:41 AM
To: [log in to unmask]
Subject: [ccp4bb] Looking for PDB His-tag statistics
Dear all,
Best wishes for the new year!
I am looking for some statistics about the fraction of protein structures in the pdb that are actually crystallized with a His tag, and from those crystallized with a His tag whether these construct were engineered with a cleavable tag or not. Has anybody done such an analysis and would want to share the outcome?
In the mean time I will mentally prepare myself for re-freshing my perl knowledge to write a script to do such an analysis. Any suggestions on how to quickly analyse this would be appreciated.
cheers
Arjan
Arjan (Harm Jan) Snijder
Associate Principal Scientist
Astra Zeneca R&D, Mölndal
Discovery Enabling Sciences and Capabilities, DECS
SE-431 83 Mölndal Sweden
tel: ++46 31 7763691
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