[ccp4bb] PhD studentship in Edinburgh
I am currently looking for a PhD student to work on structure/function studies of high-pressure adaptation by X-ray crystallography and electron microscopy coupled to single particle analysis. The research work will be carried out at the School of Biological Sciences (SBS) and at the Centre for Science at Extreme Conditions (CSEC) in Edinburgh. State-of-the art equipment for protein expression, purification and characterization and for high-pressure studies is available. Excellent X-ray crystallography facilities are also in place. The SBS has a strong interest in furthering its current electron microscopy resources. Funding would be available for UK nationals or EU nationals with at least 3 years permanent residence in the UK. Please contact Dr Laura Spagnolo (lspag...@staffmail.ed.ac.uk) for informal enquiries. Best regards, Laura -- Dr Laura Spagnolo Institute of Structural Molecular Biology Room 702/705, Darwin Building King's Buildings Mayfield Road University of Edinburgh Edinburgh EH9 3JR United Kingdom T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
[ccp4bb] protein folds
Dear Folks, The last novel proteins fold were from the yr 2007(pdb statistics), >From 2007 to till date no novel fold has been identified, this mean the present 1283 fold are the final or should I wait, if so , with what criteria do I expect for a new fold..or what are the expectations ... If we have solved 56066 structures till now with 1283 folds already known, Does it mean we have gained some rationality in defining new folds(at least a clue) ? S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.
Re: [ccp4bb] SCALA failed message
Thank you Graeme. I have installed ccp4 6.1.1 and ran the same job on SCALA succesfully. J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page: - Original Message From: Graeme Winter To: James Foadi Cc: CCP4BB@jiscmail.ac.uk Sent: Tuesday, 24 February, 2009 18:51:16 Subject: Re: [ccp4bb] SCALA failed message Hi James, You are the victim of an epic command line. This has been fixed in the 6.1.1 release, but you will find that using a shorter path (i.e. noniso rather than non-isomorphism &c.) will pull the command line down to something more sensible. CCP4i writes this out to allow the job to be rerun in a comment, but the comment is too long for Scala! Cheers, Graeme 2009/2/24 James Foadi : > Dear all, > I am running SCALA using ccp4i. The generated command file is: > > > > > > *** > /tmp/james/NONISO_insulin_from_liz_6_2_com.tmp > *** > title Scale merged insulin_from_liz _ Datasets in1, in2, in3, in4, in5 > run 1 - >INCLUDE batch 1 to 100 > run 2 - >INCLUDE batch 201 to 380 > run 3 - >INCLUDE batch 401 to 522 > run 4 - >INCLUDE batch 601 to 651 > run 5 - >INCLUDE batch 701 to 720 > RUN 2 reference > name run 1 project New crystal New dataset New > name run 2 project New crystal New dataset New > name run 3 project New crystal New dataset New > name run 4 project New crystal New dataset New > name run 5 project New crystal New dataset New > exclude EMAX - >10.0 > partials - >check - >test 0.95 1.05 - >nogap > intensities INTEGRATED - >PARTIALS > final PARTIALS > scales - >rotation SPACING 5 - >secondary 6 - >bfactor ON - >BROTATION SPACING 20 > UNFIX V > FIX A0 > UNFIX A1 > initial MEAN > tie surface 0.001 > tie bfactor 0.3 > cycles 10 converge 0.3 reject 2 > output AVERAGE > print brief nooverlap > RSIZE 80 > ## This script run with the command ## > # /home/james/build/ccp4-6.1.0/bin/scala HKLIN > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/exp_01/in1_in2_in3_in4_in5_MS_1_001.mtz" > HKLOUT "/tmp/james/NONISO_insulin_from_liz_6_1_mtz.tmp" SCALES > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6.scala" > ROGUES > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogues.log" > NORMPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_normplot.xmgr" > ANOMPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_anomplot.xmgr" > PLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_surface_plot.plt" > CORRELPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_correlplot.xmgr" > ROGUEPLOT > > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogueplot.xmgr" > > > > Unfortunately SCALA stops immediately with the following error message: > > > - > ** Unrecognized keyword ** > > RUN command must come before SCALES definition > > ** Missing or illegal value ** > - > > Any idea on what's wrong? I have to say, I had run this before with similar > data (up to 4 runs), and had never this problem. > > Thank you! > > J > > Dr James Foadi PhD > Membrane Protein Laboratory > Diamond Light Source Ltd. > Diamond House > Harwell Science and Innovation Campus > Didcot > Oxfordshire > OX11 0DE > United Kingdom > > > office email: james.fo...@diamond.ac.uk > alternative email: j.fo...@imperial.ac.uk > web page: > > > > >
Re: [ccp4bb] protein folds
Jayashankar wrote: Dear Folks, Dear gmail-user, The last novel proteins fold were from the yr 2007(pdb statistics), From 2007 to till date no novel fold has been identified, this mean the present 1283 fold are the final or should I wait, if so , with what criteria do I expect for a new fold..or what are the expectations ... [snip] Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw them at the map on the board. Take off the blindfold and investigate where the darts hit. Did you hit all the towns and cities? You hit London, Birmingham and Leeds almost certainly. But what about Brighton, did you get that? How about Clitheroe, was that hit? (Does Clitheroe count anyway or is that just another part of Preston?) I hope that that provides you some with insight. Paul.
Re: [ccp4bb] protein folds
But provided if i colud follow a pattern even blindfolded could come up with some probable things. Is it not ok to have principle of mathematical induction. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Wed, Feb 25, 2009 at 7:07 PM, Paul Emsley wrote: > Jayashankar wrote: > >> Dear Folks, >> > > Dear gmail-user, > > >> The last novel proteins fold were from the yr 2007(pdb statistics), >> From 2007 to till date no novel fold has been identified, this mean the >> present 1283 fold are the final or >> should I wait, if so , with what criteria do I expect for a new fold..or >> what are the expectations ... [snip] >> > > > Here's an experiment: > > Find a blindfold and put it on. Oh, but before you do that, take a > map of England and place it on a dartboard. > > Now take 56066 darts and throw them at the map on the board. > > Take off the blindfold and investigate where the darts hit. Did you > hit all the towns and cities? You hit London, Birmingham and Leeds > almost certainly. But what about Brighton, did you get that? How > about Clitheroe, was that hit? (Does Clitheroe count anyway or is > that just another part of Preston?) > > I hope that that provides you some with insight. > > Paul. >
Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli
Thanks to all who responded. Actually, this bulletin board is better for help with molecular biology than the molecular biology bulletin board I am subscribed to! On Tue, Feb 24, 2009 at 7:47 PM, Stephen Weeks wrote: > Mo, > Just to add my 50 cents, I didn't see any mention of the use of fusion > proteins in your original post. GST, MBP or my personal, and completely > biased, favourite SUMO (plus many more proteins) have been shown to enhance > expression when fused to the amino terminus of a target protein. If you fear > you have toxicity, simply tracking the OD600 pre and post induction normally > tell you if this is happening. I've worked with proteins that basically > baselined the cell growth upon induction and, as Artem stated, at least I > knew my protein was being made albeit at very low levels. > > Stephen > > -- > Stephen Weeks, Ph. D. > Drexel University College of Medicine > Department of Biochemistry and Molecular Biology > Room 10102 New College Building > 245 N. 15th St. > Philadelphia, PA 19102 > > Phone: (+) 215-762-7316 > Fax: (+) 215-762-4452 > > > > Mo Wong wrote: > >> I thought I'd post this to the CCP4bb, as judging by previous posts, it >> seems I could get some useful insight into my problem... >> >> This is question has probably been asked by people for a long as molecular >> biology has been around, but hopefully my question isn't a complete rehash >> of other peoples: I am trying to express a human protein in bacteria where >> the only modified amino acids are 3 phosphorylated serines. I’ve gone >> through the usual hoopla of trying to get it expressed in E. coli >> (Rosetta/Codon+ cells, varying IPTG, low temperature, etc). Sequencing >> confirms my insert is correct, but from coomassie gel inspection, I appear >> to get near zero induction (I need to do a Western to get a clearer >> assessment). I’ve heard about custom gene synthesis, and it appears Mr. Gene >> (https://www.mrgene.com/) would be a good avenue to look into as they >> optimize the ORF taking into account codon usage in E. coli (though I’m not >> sure they examine putative mRNA substructure formation like some companies >> do). It’s only 49c per base pair, so doesn’t seem too cost prohibitive. My >> only concern is that if this protein is toxic, I could be wasting money. >> >> So I was wondering, has anyone seen the expression for a particular >> protein change from zero in Rosetta/Codon+ cells using "native" sequeneces >> to being largely overexpressed in BL21(DE3) cells using codon optimized >> sequences? For folks who have had a similar problem to the one I've >> described, would you recommend that I first try using a codon optimized >> sequence in E. coli over testing protein expression in yeast/insect cells, >> or the other way round? >> >> Thanks! >> >
Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli
Did you not know that the CCP4BB-- even when all else appears to be melting down-- is Nature's sustained gift to humankind? Did you also not know that astronauts, astronomers, astrologers, artists, musicians, sportsmen, scientists, politicians, writers and everyone else subscribes to the board Given the breadth of knowledge of the CCP4BBers, molecular biology is still down the CCP4BBer's alley! Doesn't shock me that some molecular biologists responded :) The questions usually boils down to: To respond or not to respond? Cheers, Raji On Feb 25, 2009, at 2:48 PM, Mo Wong wrote: Thanks to all who responded. Actually, this bulletin board is better for help with molecular biology than the molecular biology bulletin board I am subscribed to! On Tue, Feb 24, 2009 at 7:47 PM, Stephen Weeks wrote: Mo, Just to add my 50 cents, I didn't see any mention of the use of fusion proteins in your original post. GST, MBP or my personal, and completely biased, favourite SUMO (plus many more proteins) have been shown to enhance expression when fused to the amino terminus of a target protein. If you fear you have toxicity, simply tracking the OD600 pre and post induction normally tell you if this is happening. I've worked with proteins that basically baselined the cell growth upon induction and, as Artem stated, at least I knew my protein was being made albeit at very low levels. Stephen -- Stephen Weeks, Ph. D. Drexel University College of Medicine Department of Biochemistry and Molecular Biology Room 10102 New College Building 245 N. 15th St. Philadelphia, PA 19102 Phone: (+) 215-762-7316 Fax: (+) 215-762-4452 Mo Wong wrote: I thought I'd post this to the CCP4bb, as judging by previous posts, it seems I could get some useful insight into my problem... This is question has probably been asked by people for a long as molecular biology has been around, but hopefully my question isn't a complete rehash of other peoples: I am trying to express a human protein in bacteria where the only modified amino acids are 3 phosphorylated serines. I’ve gone through the usual hoopla of trying to get it expressed in E. coli (Rosetta/Codon+ cells, varying IPTG, low temperature, etc). Sequencing confirms my insert is correct, but from coomassie gel inspection, I appear to get near zero induction (I need to do a Western to get a clearer assessment). I’ve heard about custom gene synthesis, and it appears Mr. Gene (https://www.mrgene.com/) would be a good avenue to look into as they optimize the ORF taking into account codon usage in E. coli (though I’m not sure they examine putative mRNA substructure formation like some companies do). It’s only 49c per base pair, so doesn’t seem too cost prohibitive. My only concern is that if this protein is toxic, I could be wasting money. So I was wondering, has anyone seen the expression for a particular protein change from zero in Rosetta/Codon+ cells using "native" sequeneces to being largely overexpressed in BL21(DE3) cells using codon optimized sequences? For folks who have had a similar problem to the one I've described, would you recommend that I first try using a codon optimized sequence in E. coli over testing protein expression in yeast/insect cells, or the other way round? Thanks!
Re: [ccp4bb] protein folds
On Wednesday 25 February 2009 08:20:14 Jayashankar wrote: > Dear Folks, > > The last novel proteins fold were from the yr 2007(pdb statistics), > From 2007 to till date no novel fold has been identified, If you reached this conclusion by looking at the PDB web site, you should note that the site explains these numbers are taken from SCOP. The SCOP website states that the most recent update was some time in 2007. So you would have to look elsewhere for new folds deposited since mid-2007. > this mean the > present 1283 fold are the final or > should I wait, if so , with what criteria do I expect for a new fold..or > what are the expectations ... > > If we have solved 56066 structures till now with 1283 folds already known, > Does it mean we have gained some rationality in defining new folds(at least > a clue) ? > > S.Jayashankar > Research Student > Institute for Biophysical Chemistry > Hannover Medical School > Germany. > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] protein folds
As an outsider to this field, it would seem another way to approach it would be to ask, of the currently known folds, how many have only one member (excluding evolutionarily related protein families)? If a large number of folds have only been sampled once, it is likely that there are others that have not been sampled at all. If every known fold has at least 5 independently-evolved examples solved, then it is less likely that some have been missed. If at this stage there are still many folds with only one known example, then probably in fact many folds are represented by a single protein family, in which case it will be necessary to solve a representative from every family to be sure we're not missing a fold. Paul Emsley wrote: Jayashankar wrote: Dear Folks, Dear gmail-user, The last novel proteins fold were from the yr 2007(pdb statistics), From 2007 to till date no novel fold has been identified, this mean the present 1283 fold are the final or should I wait, if so , with what criteria do I expect for a new fold..or what are the expectations ... [snip] Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw them at the map on the board. Take off the blindfold and investigate where the darts hit. Did you hit all the towns and cities? You hit London, Birmingham and Leeds almost certainly. But what about Brighton, did you get that? How about Clitheroe, was that hit? (Does Clitheroe count anyway or is that just another part of Preston?) I hope that that provides you some with insight. Paul.
Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli
I agree with the accolades given by Raji to the CCPBB, but suggest a difference: it is not given by "Nature," or any other polytheistic entity but rather by the patience and sustained efforts of all the souls who resist the urge to excoriate, which I would guess scales linearly to the number of years on the BB. Thanks to all of you who help out for little to no reward, Jacob *** 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: j-kell...@northwestern.edu *** - Original Message - From: Raji Edayathumangalam To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, February 25, 2009 2:01 PM Subject: Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli Did you not know that the CCP4BB-- even when all else appears to be melting down-- is Nature's sustained gift to humankind? Did you also not know that astronauts, astronomers, astrologers, artists, musicians, sportsmen, scientists, politicians, writers and everyone else subscribes to the board Given the breadth of knowledge of the CCP4BBers, molecular biology is still down the CCP4BBer's alley! Doesn't shock me that some molecular biologists responded :) The questions usually boils down to: To respond or not to respond? Cheers, Raji On Feb 25, 2009, at 2:48 PM, Mo Wong wrote: Thanks to all who responded. Actually, this bulletin board is better for help with molecular biology than the molecular biology bulletin board I am subscribed to! On Tue, Feb 24, 2009 at 7:47 PM, Stephen Weeks wrote: Mo, Just to add my 50 cents, I didn't see any mention of the use of fusion proteins in your original post. GST, MBP or my personal, and completely biased, favourite SUMO (plus many more proteins) have been shown to enhance expression when fused to the amino terminus of a target protein. If you fear you have toxicity, simply tracking the OD600 pre and post induction normally tell you if this is happening. I've worked with proteins that basically baselined the cell growth upon induction and, as Artem stated, at least I knew my protein was being made albeit at very low levels. Stephen -- Stephen Weeks, Ph. D. Drexel University College of Medicine Department of Biochemistry and Molecular Biology Room 10102 New College Building 245 N. 15th St. Philadelphia, PA 19102 Phone: (+) 215-762-7316 Fax: (+) 215-762-4452 Mo Wong wrote: I thought I'd post this to the CCP4bb, as judging by previous posts, it seems I could get some useful insight into my problem... This is question has probably been asked by people for a long as molecular biology has been around, but hopefully my question isn't a complete rehash of other peoples: I am trying to express a human protein in bacteria where the only modified amino acids are 3 phosphorylated serines. I’ve gone through the usual hoopla of trying to get it expressed in E. coli (Rosetta/Codon+ cells, varying IPTG, low temperature, etc). Sequencing confirms my insert is correct, but from coomassie gel inspection, I appear to get near zero induction (I need to do a Western to get a clearer assessment). I’ve heard about custom gene synthesis, and it appears Mr. Gene (https://www.mrgene.com/) would be a good avenue to look into as they optimize the ORF taking into account codon usage in E. coli (though I’m not sure they examine putative mRNA substructure formation like some companies do). It’s only 49c per base pair, so doesn’t seem too cost prohibitive. My only concern is that if this protein is toxic, I could be wasting money. So I was wondering, has anyone seen the expression for a particular protein change from zero in Rosetta/Codon+ cells using "native" sequeneces to being largely overexpressed in BL21(DE3) cells using codon optimized sequences? For folks who have had a similar problem to the one I've described, would you recommend that I first try using a codon optimized sequence in E. coli over testing protein expression in yeast/insect cells, or the other way round? Thanks!
Re: [ccp4bb] protein folds
What happens when a single protein strays from the fold? Jacob - Original Message - From: "Edward A. Berry" To: Sent: Wednesday, February 25, 2009 2:48 PM Subject: Re: [ccp4bb] protein folds As an outsider to this field, it would seem another way to approach it would be to ask, of the currently known folds, how many have only one member (excluding evolutionarily related protein families)? If a large number of folds have only been sampled once, it is likely that there are others that have not been sampled at all. If every known fold has at least 5 independently-evolved examples solved, then it is less likely that some have been missed. If at this stage there are still many folds with only one known example, then probably in fact many folds are represented by a single protein family, in which case it will be necessary to solve a representative from every family to be sure we're not missing a fold. Paul Emsley wrote: Jayashankar wrote: Dear Folks, Dear gmail-user, The last novel proteins fold were from the yr 2007(pdb statistics), From 2007 to till date no novel fold has been identified, this mean the present 1283 fold are the final or should I wait, if so , with what criteria do I expect for a new fold..or what are the expectations ... [snip] Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw them at the map on the board. Take off the blindfold and investigate where the darts hit. Did you hit all the towns and cities? You hit London, Birmingham and Leeds almost certainly. But what about Brighton, did you get that? How about Clitheroe, was that hit? (Does Clitheroe count anyway or is that just another part of Preston?) I hope that that provides you some with insight. Paul.
Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli
Some useful tips to try can be found at http://www.embl-hamburg.de/services/protein/production/expression/optimising_exprlevels.html I've had a recent case where an untagged protein (part of a complex) was not expressed at all but expressed well when tagged at the N-terminal with His6 or MBP. Also try changing from an N-terminal to C-terminal tag (or vice-versa). ho UC Berkeley
Re: [ccp4bb] protein folds
The protein wolves get it - and it's never heard from or seen again. Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Wednesday, February 25, 2009 4:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] protein folds What happens when a single protein strays from the fold? Jacob - Original Message - From: "Edward A. Berry" To: Sent: Wednesday, February 25, 2009 2:48 PM Subject: Re: [ccp4bb] protein folds > As an outsider to this field, it would seem another way to approach it > would be to ask, of the currently known folds, how many have only one > member (excluding evolutionarily related protein families)? > > If a large number of folds have only been sampled once, it is likely > that there are others that have not been sampled at all. If every known > fold has at least 5 independently-evolved examples solved, then it is > less likely that some have been missed. > > If at this stage there are still many folds with only one known example, > then probably in fact many folds are represented by a single protein > family, in which case it will be necessary to solve a representative from > every family to be sure we're not missing a fold. > > > Paul Emsley wrote: >> Jayashankar wrote: >>> Dear Folks, >> >> Dear gmail-user, >> >>> >>> The last novel proteins fold were from the yr 2007(pdb statistics), >>> From 2007 to till date no novel fold has been identified, this mean >>> the present 1283 fold are the final or >>> should I wait, if so , with what criteria do I expect for a new >>> fold..or what are the expectations ... [snip] >> >> >> Here's an experiment: >> >> Find a blindfold and put it on. Oh, but before you do that, take a >> map of England and place it on a dartboard. >> >> Now take 56066 darts and throw them at the map on the board. >> >> Take off the blindfold and investigate where the darts hit. Did you >> hit all the towns and cities? You hit London, Birmingham and Leeds >> almost certainly. But what about Brighton, did you get that? How >> about Clitheroe, was that hit? (Does Clitheroe count anyway or is >> that just another part of Preston?) >> >> I hope that that provides you some with insight. >> >> Paul. >> >
Re: [ccp4bb] protein folds
Unfortunately the database contains huge bias towards: a) proteins that are easy to make and crystallize b) biologically interesting protein families Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Edward A. Berry Sent: Wednesday, February 25, 2009 3:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] protein folds As an outsider to this field, it would seem another way to approach it would be to ask, of the currently known folds, how many have only one member (excluding evolutionarily related protein families)? If a large number of folds have only been sampled once, it is likely that there are others that have not been sampled at all. If every known fold has at least 5 independently-evolved examples solved, then it is less likely that some have been missed. If at this stage there are still many folds with only one known example, then probably in fact many folds are represented by a single protein family, in which case it will be necessary to solve a representative from every family to be sure we're not missing a fold. Paul Emsley wrote: > Jayashankar wrote: >> Dear Folks, > > Dear gmail-user, > >> >> The last novel proteins fold were from the yr 2007(pdb statistics), >> From 2007 to till date no novel fold has been identified, this mean >> the present 1283 fold are the final or >> should I wait, if so , with what criteria do I expect for a new >> fold..or what are the expectations ... [snip] > > > Here's an experiment: > > Find a blindfold and put it on. Oh, but before you do that, take a > map of England and place it on a dartboard. > > Now take 56066 darts and throw them at the map on the board. > > Take off the blindfold and investigate where the darts hit. Did you > hit all the towns and cities? You hit London, Birmingham and Leeds > almost certainly. But what about Brighton, did you get that? How > about Clitheroe, was that hit? (Does Clitheroe count anyway or is > that just another part of Preston?) > > I hope that that provides you some with insight. > > Paul. >
Re: [ccp4bb] protein folds
Paul Emsley wrote: Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw them at the map on the board. Take off the blindfold and investigate where the darts hit. Did you hit all the towns and cities? You hit London, Birmingham and Leeds almost certainly. But what about Brighton, did you get that? How about Clitheroe, was that hit? (Does Clitheroe count anyway or is that just another part of Preston?) I hope that that provides you some with insight. Paul. I discovered recently that there is a little town/village called "Holton" just outside of Oxford. I doubt it would have been hit by one of Paul's darts as I, myself, was completely unaware of its existence until I was looking at a "local" map of Oxford only last month. It is an amazingly little place. Only one road, one church and a village hall with my name on it. Perhaps in the grand scheme of things, "Holton" is not worthy of much note, but it was still very interesting to me. -James Holton MAD Scientist
Re: [ccp4bb] protein folds
Must be even smaller than Daresbury then. They don't even have a synchrotron! Bart James Holton wrote: Paul Emsley wrote: Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw them at the map on the board. Take off the blindfold and investigate where the darts hit. Did you hit all the towns and cities? You hit London, Birmingham and Leeds almost certainly. But what about Brighton, did you get that? How about Clitheroe, was that hit? (Does Clitheroe count anyway or is that just another part of Preston?) I hope that that provides you some with insight. Paul. I discovered recently that there is a little town/village called "Holton" just outside of Oxford. I doubt it would have been hit by one of Paul's darts as I, myself, was completely unaware of its existence until I was looking at a "local" map of Oxford only last month. It is an amazingly little place. Only one road, one church and a village hall with my name on it. Perhaps in the grand scheme of things, "Holton" is not worthy of much note, but it was still very interesting to me. -James Holton MAD Scientist
Re: [ccp4bb] protein folds
CCP4 bulletin board wrote on 02/25/2009 03:08:10 PM: > On Wednesday 25 February 2009 08:20:14 Jayashankar wrote: > > Dear Folks, > > > > The last novel proteins fold were from the yr 2007(pdb statistics), > > From 2007 to till date no novel fold has been identified, > > If you reached this conclusion by looking at the PDB web site, > you should note that the site explains these numbers are taken from SCOP. > The SCOP website states that the most recent update was some time in 2007. > > So you would have to look elsewhere for new folds deposited since mid-2007. > > In fact, you have to look no further than SCOP! Or should I say, pre-SCOP, the pre-release partial classification of the latest batch of proteins from the PDB. Here's the webpage: http://www.mrc-lmb.cam.ac.uk/agm/pre-scop/ This says that they're still classifying proteins deposited as recently as Oct 2008, which is a relief to me - I was worried that SCOP had been abandoned. To address the original question, here are some numbers: Folds in SCOP 1.71 (18 Jan 2005): 971 Folds in SCOP 1.73 (26 Sep 2007): 1086 Folds in pre-SCOP (Oct-ish 2008): 1392 We're not done finding new folds yet, folks... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
[ccp4bb] off-topic detergent hydrolysis?
Hi there, I am using a stock solution of Octyl-Glucoside to crystallize my membrane protein, which was made ~1 year before and kept at 4c . I wonder whether OG can be hydrolysed under this condition and whether there is a way to test. Many thanks, Deliang
Re: [ccp4bb] off-topic detergent hydrolysis?
If it smells of octanol (vaguely fruity, cloying odor) and possibly has a little phase separation (octanol poorly mixes with water) then you have significant hydrolysis. Beyond the smell test, you can run a small sample out on a TLC with n-Octanol as control lane. Pretty easy. As to whether BOG can be hydrolyzed in your specific case - that entirely depends on the conditions (primarily the pH). Contamination by glycosyl hydrolases can be an issue too but why would you have something like that? Normally octanol contamination is found in poorly purified (technical grade) octyl glucoside preparations (which typically also contain a mixture of alpha and beta anomers). In my experience solutions of pure BOG in water at neutral pH are stable (although to be fair I've never tested for a whole year). Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. _ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of deliang Sent: Wednesday, February 25, 2009 9:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic detergent hydrolysis? Hi there, I am using a stock solution of Octyl-Glucoside to crystallize my membrane protein, which was made ~1 year before and kept at 4c . I wonder whether OG can be hydrolysed under this condition and whether there is a way to test. Many thanks, Deliang
