Re: [ccp4bb] zinc fingre
Dear All, Thanks everyone for the suggestions. I did go to library to look up some chapters in books which gave me lot of information about conserved zinc finger domain. My protein has Cx4C and Cx3C and with very large spacing, so I suspect it could be zinc finger like protein (though no software showed any indication) but I am looking forward to do some experiments to confirm this. I was looking for some examples other than known domains (TFIIS, LIM, ring finger ref:encyclopedia of Mol Biol and Mol Med vol 6) which have C2H2 or C3H but doesn't follow the rules zinc finger but still bind to DNA and has been crystallized. I guess I will do more reading. Thanks againRajesh Date: Wed, 4 Apr 2012 00:43:48 +0100 From: hsuu...@u.washington.edu Subject: Re: zinc fingre To: CCP4BB@JISCMAIL.AC.UK; ccp4...@hotmail.com Hi Rajesh, Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already. Best, Peter
Re: [ccp4bb] zinc fingre
Yes, Rajesh, I completely agree with Pius. There is absolutely nothing wrong in asking a question on ccp4bb. The suggestion 'read a book and search on-line information sources' is a good one on any subject. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pius Padayatti Sent: Tuesday, April 03, 2012 11:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] zinc fingre Hi Rajesh, First of all you did the right thing to ask people here about our doubts. There is nothing wrong in asking questions. The board is for asking questions realted to crystallography (all aspects). Padayatti On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] zinc fingre
Hi Rajesh, Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already. Best, Peter
[ccp4bb] zinc fingre
Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals.It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only).Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well?I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks,Rajesh
Re: [ccp4bb] zinc fingre
Read a book. If you can't find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh
Re: [ccp4bb] zinc fingre
Thanks.. I will. Date: Tue, 3 Apr 2012 15:17:34 + From: debas...@uab.edu Subject: Re: [ccp4bb] zinc fingre To: CCP4BB@JISCMAIL.AC.UK Read a book. If you can’t find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh
Re: [ccp4bb] zinc fingre
Hi Rajesh, First of all you did the right thing to ask people here about our doubts. There is nothing wrong in asking questions. The board is for asking questions realted to crystallography (all aspects). Padayatti On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh -- Pius S Padayatti,PhD, Phone: 216-658-4528
