Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
Chris, Can you or others speculate, perhaps in light of the structure, why a his-tag would cause precipitation? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Christopher Bahl [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, November 11, 2008 10:06 AM Subject: Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags Hi Jorge, We have had cases both for and against leaving His-tags on proteins. In one case, the presence of the His-tag was causing the protein to precipitate, blocking our attempts at crystallization until we removed it. However, we also had a different protein that crystallized beautifully with the His-tag left on. I can't speak to the impact the tag had on crystallization since we never bothered to remove it and it was not visible in the structure. My (rather unhelpful) input is that it greatly depends on the individual protein as to whether or not it is beneficial to remove the His-tag prior to crystallization. -Chris Tim Gruene wrote: Hi Jorge, using a system where you can cleave off the His-tag (with TEV, FactorX, etc) adds a purification step which is complementary to the first purification step (Ni-column etc). In my experience this results in very pure protein which makes it more likely to crystallise. Therefore I would always choose such a system and not spend much time on trying to crystallise the protein with the His-tag attached. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 11 Nov 2008, [EMAIL PROTECTED] wrote: Dear all, Concerning the crystallization of proteins with a His-tag, based upon discussions on this bulletin board and on the article Mike Carson, David H. Johnson, Heather McDonald, Christie Brouillette and Lawrence J. DeLucas, His-tag impact on structure, Acta Cryst. D63, 295-301, (2007). I understand that as a general approach one should try to crystallize the protein with the His-tag (yet it might crystallize, so no need to care the work of taking out the tag); then, if this is not successful, go to the procedure to either express (and purify) it without the His tag or take it out later. Any observations/advices? But one other question to add is what if the protein is expressed with both a c-myc tag and a His-tag (you might consider also the case in which only the c-myc tag is present). Any experience on the effect of the c-myc tag on crystallization? References are welcome yet I could not find much googling around... Thanks, Jorge
Re: [ccp4bb] low B factors
Hi Jan, Did you use the TLS refinement for your data? I have had the similar problem with the multi-group TLS refinement. After the first run the resulting pdb file contained unreasonably small atomic B factors for many atoms comparing to the Wilson plot B factor. They seemed to be the TLS-B factors instead of the expected residual B factors. The TLSANL could have not produced the total nor residual B factors when given that file (plus the .tls file from that Refmac run). Moreover, I couldn't use this file as an input for the next Refmac refinement as it was not stable. Interestingly, I have had no problem when using one group only in the TLS step. The version of Refmac was 5.2.0019. Do you observe by chance a similar case? Aleks On 11 Nov 2008, at 01:36, Jan Abendroth wrote: Hi all, I have a number of low-ish resolution data sets that show a strange B-factor behaviour: All are just better than 3AA resolution, collected on a strong synchrotron beamline. Some, yet not tremendous radiation decay. Wilson scaling, obviously not very reliable at this resolution, gives me a Wilson B of about 40, already a low number. Refinement in refmac5 (5.5.0053) with individual B-factors refinement leads to an average B factor of around 16 with several individual B factors hitting the B=2 limit... When I convert Is to Fs in truncate simply using the square root, things get even a bit worse, the average B now is 14. When I try to do an overall B-factor refinement, still individual B-factors appear in the output file. refinement details: 2.8AA resolution,medium ncs for two ncs related chains, no riding hydrogens, simple scaling, MKLF target, isotropic B factors Rwork: 0.206, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I could retrain a bit more... Any ideas how to handle this? Basically, my question is: how do I get the overall B factor to realistic numbers? Thanks a lot for any hints Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com -- Aleksander W. Roszak, PhD E-mail: [EMAIL PROTECTED] Protein Crystallography Web: www.chem.gla.ac.uk/~aleks University of Glasgow Fax: +44-(0)141-330 3779 Level 3 Room B 317 Tel (office): +44-(0)141-330 4476 Glasgow Biomedical Research Centre Tel (X-ray lab): +44-(0)141-330 3589 120 University PlaceMobile: +44-(0)780 9559996 Glasgow G12 8TA Scotland, UK
[ccp4bb] MRC Grant Opportunities the Research Complex at Harwell (not relevant to non-UK CCP4BBers)
Dear CCP4BBers, With apologies to non-UK crystallographers (to whom it is not relevant so they should read no further). Just to let you know that there are opportunities for grant and fellowship applications from researchers wishing to work in the Research Complex at Harwell (RCaH). This is a great new lab being built next door to Diamond, which is a prime spot for PX since it will also house the CCP4 core team and the Oxford Protein Production Facility (OPPF). A call has just gone out from MRC, and the other Research Councils have/will have schemes (e.g. the BBSRC Diamond Fellowship scheme, which is closing soon, but there will be other calls). Full information of the MRC calls can be found on the website: http://www.mrc.ac.uk/ApplyingforaGrant/CallsForProposals/RCaH/index.htm. General info on RCaH on www.mrc.ac.uk/OurResearch/ResourcesforScientists/ResearchComplex --- | Simon E.V. Phillips | --- Director, Research Complex at Harwell (RCaH) Diamond Light Source Ltd Diamond House Chilton Didcot Oxon OX11 0DE United Kingdom Email: [EMAIL PROTECTED] Tel: +44 (0)1235 778946 +44 (0)1235 778431 (sec) +44 (0)7884 436011 (mobile) www: www.mrc.ac.uk/OurResearch/ResourcesforScientists/ResearchComplex Visiting Professor of Biophysics Astbury Centre for Structural Molecular Biology University of Leeds Visiting Professor in Molecular Biophysics Department of Biochemistry University of Oxford
Re: [ccp4bb] low B factors
It might be possible that there's a problem in the low resolution portion of your data. You could check the wilson plot to make sure it looks normal at that range, and possibly change the low-resolution cutoff refmac is using. Pete Jan Abendroth wrote: Hi all, I have a number of low-ish resolution data sets that show a strange B-factor behaviour: All are just better than 3AA resolution, collected on a strong synchrotron beamline. Some, yet not tremendous radiation decay. Wilson scaling, obviously not very reliable at this resolution, gives me a Wilson B of about 40, already a low number. Refinement in refmac5 (5.5.0053) with individual B-factors refinement leads to an average B factor of around 16 with several individual B factors hitting the B=2 limit... When I convert Is to Fs in truncate simply using the square root, things get even a bit worse, the average B now is 14. When I try to do an overall B-factor refinement, still individual B-factors appear in the output file. refinement details: 2.8AA resolution,medium ncs for two ncs related chains, no riding hydrogens, simple scaling, MKLF target, isotropic B factors Rwork: 0.206, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I could retrain a bit more... Any ideas how to handle this? Basically, my question is: how do I get the overall B factor to realistic numbers? Thanks a lot for any hints Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
[ccp4bb] meeting and job
dear bbers 1. the full programme for the BSG BCA winter meeting is now available from a link at the bottom of this web page: http://conferences.ncl.ac.uk/BCA_BSG_Winter_2008/programme.html registration is open! and please note the generosity of our sponsors has enabled registration costs to be kept as low as possible. 2. there are a few more days before the closing date for a post-doc position in my lab, providing core support to me and colleagues. success in the post will be reflected in publications - the previous postholder has had publications in Science, Nature, JACS, JBC, JMB in 2008 alone. http://www15.i-grasp.com/fe/tpl_newcastle02.asp?s=oxgIfLQnAyPBgDdPyvjobid=27132,2336340298key=2596529c=334765235614pagestamp=seyuocvmwcbprshjdd rick -- R. J. Lewis Professor of Structural Biology Institute for Cell and Molecular Biosciences Faculty of Medical Sciences Tel: +44 (0)191 222 5482 University of Newcastle Fax: +44 (0)191 222 7424 Newcastle upon Tyne, NE2 4HH, UKEmail: [EMAIL PROTECTED]
Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
Hi Jorge, using a system where you can cleave off the His-tag (with TEV, FactorX, etc) adds a purification step which is complementary to the first purification step (Ni-column etc). In my experience this results in very pure protein which makes it more likely to crystallise. Therefore I would always choose such a system and not spend much time on trying to crystallise the protein with the His-tag attached. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 11 Nov 2008, [EMAIL PROTECTED] wrote: Dear all, Concerning the crystallization of proteins with a His-tag, based upon discussions on this bulletin board and on the article Mike Carson, David H. Johnson, Heather McDonald, Christie Brouillette and Lawrence J. DeLucas, His-tag impact on structure, Acta Cryst. D63, 295-301, (2007). I understand that as a general approach one should try to crystallize the protein with the His-tag (yet it might crystallize, so no need to care the work of taking out the tag); then, if this is not successful, go to the procedure to either express (and purify) it without the His tag or take it out later. Any observations/advices? But one other question to add is what if the protein is expressed with both a c-myc tag and a His-tag (you might consider also the case in which only the c-myc tag is present). Any experience on the effect of the c-myc tag on crystallization? References are welcome yet I could not find much googling around... Thanks, Jorge
[ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
Dear all, Concerning the crystallization of proteins with a His-tag, based upon discussions on this bulletin board and on the article Mike Carson, David H. Johnson, Heather McDonald, Christie Brouillette and Lawrence J. DeLucas, His-tag impact on structure, Acta Cryst. D63, 295-301, (2007). I understand that as a general approach one should try to crystallize the protein with the His-tag (yet it might crystallize, so no need to care the work of taking out the tag); then, if this is not successful, go to the procedure to either express (and purify) it without the His tag or take it out later. Any observations/advices? But one other question to add is what if the protein is expressed with both a c-myc tag and a His-tag (you might consider also the case in which only the c-myc tag is present). Any experience on the effect of the c-myc tag on crystallization? References are welcome yet I could not find much googling around... Thanks, Jorge
Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
Another theory is that trace amounts of Ni may leech off the column during purification and coordinate with multiple His-tags on the pure protein, causing them to aggregate. For sure. We had a case where a protein would precipitate after post-Ni-NTA dialysis. The precipitate would go back into solution if resuspended in the presence of imidazole or EDTA/EGTA. Inclusion of a bit of EDTA into fractions and dialysis solution completely eliminated precipitation. Dima
[ccp4bb] mtz type labels different in ccp4-6.0.99e?
Hi Is it likely that the type labels for DANO and IMEAN have been changed in the beta ccp4-6.0.99e from DANO -type - D to DANO type F IMEAN - -type - Y to IMEAN type J I am using an old sharp and it seems to be a little miffed at my DANO columns from ccp4 6.0.99e being of type F Thanks in advance Hari
Re: [ccp4bb] mtz type labels different in ccp4-6.0.99e?
This is a bug in the 99e ctruncate, since fixed. You should use the old truncate for now Phil On 11 Nov 2008, at 17:16, hari jayaram wrote: Hi Is it likely that the type labels for DANO and IMEAN have been changed in the beta ccp4-6.0.99e from DANO -type - D to DANO type F IMEAN - -type - Y to IMEAN type J I am using an old sharp and it seems to be a little miffed at my DANO columns from ccp4 6.0.99e being of type F Thanks in advance Hari
Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
Hi Jorge, We have had cases both for and against leaving His-tags on proteins. In one case, the presence of the His-tag was causing the protein to precipitate, blocking our attempts at crystallization until we removed it. However, we also had a different protein that crystallized beautifully with the His-tag left on. I can't speak to the impact the tag had on crystallization since we never bothered to remove it and it was not visible in the structure. My (rather unhelpful) input is that it greatly depends on the individual protein as to whether or not it is beneficial to remove the His-tag prior to crystallization. -Chris Tim Gruene wrote: Hi Jorge, using a system where you can cleave off the His-tag (with TEV, FactorX, etc) adds a purification step which is complementary to the first purification step (Ni-column etc). In my experience this results in very pure protein which makes it more likely to crystallise. Therefore I would always choose such a system and not spend much time on trying to crystallise the protein with the His-tag attached. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 11 Nov 2008, [EMAIL PROTECTED] wrote: Dear all, Concerning the crystallization of proteins with a His-tag, based upon discussions on this bulletin board and on the article Mike Carson, David H. Johnson, Heather McDonald, Christie Brouillette and Lawrence J. DeLucas, His-tag impact on structure, Acta Cryst. D63, 295-301, (2007). I understand that as a general approach one should try to crystallize the protein with the His-tag (yet it might crystallize, so no need to care the work of taking out the tag); then, if this is not successful, go to the procedure to either express (and purify) it without the His tag or take it out later. Any observations/advices? But one other question to add is what if the protein is expressed with both a c-myc tag and a His-tag (you might consider also the case in which only the c-myc tag is present). Any experience on the effect of the c-myc tag on crystallization? References are welcome yet I could not find much googling around... Thanks, Jorge
Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags
In our case, incubation in the presence of imidazole can knock the protein out of solution- this was gleaned from crystallization conditions containing imidazole. The best we could come up with is that the imidazole groups from the His-tag were interacting with neighboring protein in solution, causing them to precipitate. Another theory is that trace amounts of Ni may leech off the column during purification and coordinate with multiple His-tags on the pure protein, causing them to aggregate. Hope that helps, -Chris Jacob Keller wrote: Chris, Can you or others speculate, perhaps in light of the structure, why a his-tag would cause precipitation? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Christopher Bahl [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, November 11, 2008 10:06 AM Subject: Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags Hi Jorge, We have had cases both for and against leaving His-tags on proteins. In one case, the presence of the His-tag was causing the protein to precipitate, blocking our attempts at crystallization until we removed it. However, we also had a different protein that crystallized beautifully with the His-tag left on. I can't speak to the impact the tag had on crystallization since we never bothered to remove it and it was not visible in the structure. My (rather unhelpful) input is that it greatly depends on the individual protein as to whether or not it is beneficial to remove the His-tag prior to crystallization. -Chris Tim Gruene wrote: Hi Jorge, using a system where you can cleave off the His-tag (with TEV, FactorX, etc) adds a purification step which is complementary to the first purification step (Ni-column etc). In my experience this results in very pure protein which makes it more likely to crystallise. Therefore I would always choose such a system and not spend much time on trying to crystallise the protein with the His-tag attached. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 11 Nov 2008, [EMAIL PROTECTED] wrote: Dear all, Concerning the crystallization of proteins with a His-tag, based upon discussions on this bulletin board and on the article Mike Carson, David H. Johnson, Heather McDonald, Christie Brouillette and Lawrence J. DeLucas, His-tag impact on structure, Acta Cryst. D63, 295-301, (2007). I understand that as a general approach one should try to crystallize the protein with the His-tag (yet it might crystallize, so no need to care the work of taking out the tag); then, if this is not successful, go to the procedure to either express (and purify) it without the His tag or take it out later. Any observations/advices? But one other question to add is what if the protein is expressed with both a c-myc tag and a His-tag (you might consider also the case in which only the c-myc tag is present). Any experience on the effect of the c-myc tag on crystallization? References are welcome yet I could not find much googling around... Thanks, Jorge
