Check with Daniel which one he recommends. Mark Saper 3040 & 3250 Chemistry Building Dept of Biological Chemistry sa...@umich.edu 734 764 3353 office 734 276 6505 mobile
On Feb 26, 2012, at 7:00 PM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: > There are 8 messages totaling 1732 lines in this issue. > > Topics of the day: > > 1. Heterotetrameric protein (3) > 2. Membrane Protein Crystallization Plates > 3. Any calculation function in CCP4 to analyze coordinate file? > 4. Fwd: [ccp4bb] Membrane Protein Crystallization Plates > 5. Postdoctoral position in structure-function studies of enzymes for > biotechnologies > 6. coot with probe and reduce > > ---------------------------------------------------------------------- > > Date: Sat, 25 Feb 2012 16:26:23 -0800 > From: Koustav Maity <mai...@gmail.com> > Subject: Heterotetrameric protein > > Hi all, > > does anyone know a protein which make hetero tetramer of A2B2 which > arrange as[image: Inline image 1] and NOT as [image: Inline image 2]? > > > Its great if these proteins are small? All the hetero tetramer I found was > of [image: Inline image 3] type. > > > Thanks > > Dhiraj > > ------------------------------ > > Date: Sun, 26 Feb 2012 00:45:08 +0000 > From: "Tanner, John J." <tanne...@missouri.edu> > Subject: Re: Heterotetrameric protein > > Tryptophan synthase forms a ABBA tetramer (PDB 2J9X). It is not exactly what > you want, but it is different from what you have found. > > Jack Tanner > > John J. Tanner > Professor of Chemistry and Biochemistry > University of Missouri-Columbia > 125 Chemistry Building > Columbia, MO 65211 > email: tanne...@missouri.edu > phone: 573-884-1280 > fax: 573-882-2754 > web: http://www.chem.missouri.edu/tannergroup/tanner.html > > On Feb 25, 2012, at 6:26 PM, Koustav Maity wrote: > >> >> >> >> >> Hi all, >> >> does anyone know a protein which make hetero tetramer of A2B2 which arrange >> as<no1.png> and NOT as <no2.png>? >> >> Its great if these proteins are small? All the hetero tetramer I found was >> of <no2.png> type. >> >> >> Thanks >> >> Dhiraj >> > > ------------------------------ > > Date: Sun, 26 Feb 2012 00:42:43 +0000 > From: "Lavy, Tali" <tl...@cshl.edu> > Subject: Re: Heterotetrameric protein > > Hi Dhiraj, > > We've just submitted such a heterotetramer to the pdb (3V2U) > > Tali > ________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Koustav Maity > [mai...@gmail.com] > Sent: Saturday, February 25, 2012 7:26 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Heterotetrameric protein > > > > > > Hi all, > > does anyone know a protein which make hetero tetramer of A2B2 which arrange > as[Inline image 1] and NOT as [Inline image 2] ? > > Its great if these proteins are small? All the hetero tetramer I found was of > [Inline image 3] type. > > > Thanks > > Dhiraj > > ------------------------------ > > Date: Sat, 25 Feb 2012 20:07:50 -0500 > From: Pius Padayatti <ppadaya...@gmail.com> > Subject: Re: Membrane Protein Crystallization Plates > > Hi Yuri, > i strongly suggest these plates sold through Hampton research > Paul Marienfeld GmbH plates for your use. > here is a link , best plates in the market. > link: http://hamptonresearch.com/product_detail.aspx?cid=10&sid=182&pid=611 > > Plates comes with extra cover slips in addition to single glass cover > for four wells at a time > whcih let you set these plates manually if you like it that way. > > Good for automations as well. > only problem: since the galss is siliconized you can not write anything on it > (may be there is some industry grade marker might work.) > But there is enough place on side to stick a printed label or bar code > for your'automation > for keeping records > hope this is what you wanted to know. > > if you are money crunched and want to make some plates > on your own. buy regular micoscope slides, some two sided > tapes (3M) very thin and a tool that sold for cutting out small pieces > of tissue samples. it looks like a pen with sharp > punch enough to make a hole in a 3M tape > make a 27 hole plate in a standard microslide. > > cheers > pius > > > > > > > On Sat, Feb 25, 2012 at 3:35 PM, Yuri Pompeu <yuri.pom...@ufl.edu> wrote: >> Hello Everyone, >> I am considering the purchase of crystallization plates for membrane >> proteins. >> I would love to hear what some of the community thinks or has experienced >> with these. >> Particulalrly the monoolein and monoolein/cholesterol coated plates ( I am >> not sure I can mention the vendor here but it "should" not matter) >> So fire away. Is it worth it? Any succes stories? Bad experiences? >> I appreciate the input >> Best, >> Yuri > > > > -- > Pius S Padayatti,PhD, > Phone: 216-658-4528 > > ------------------------------ > > Date: Sun, 26 Feb 2012 14:58:43 +0100 > From: Tim Gruene <t...@shelx.uni-ac.gwdg.de> > Subject: Re: Any calculation function in CCP4 to analyze coordinate file? > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Wenhe, > > what you name 'general' may in fact be quite specific and hence running > a single program without any options provided is rather unlikely to give > the answers you seek. > > moleman2 and other USF utilities (not a ccp4 program) come closest to > what you are looking for, I guess. > > Cheers, > Tim > > > On 02/25/2012 11:59 PM, WENHE ZHONG wrote: >> Dear members, >> >> Just have a silly question past my mind: is there any program in CCP4 can >> be used to analyze coordinate file (.pdb format) to have a very >> general/overall discription about the structure? --such as the total number >> of protein residues/water/ligand, the total atoms of protein/water/ligand, >> the average b-factor of protein/water/ligand, the number of residues which >> have alternative side chians, and so on. >> >> Thank you. >> >> King regards, >> Wenhe >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPSjqNUxlJ7aRr7hoRArlyAKD5GfPxWr8At/y/8kQ7byhfbWTZogCgoXmL > +dnIgQhmPFR1w3uR4GBVtS8= > =OVKy > -----END PGP SIGNATURE----- > > ------------------------------ > > Date: Sun, 26 Feb 2012 09:33:24 -0500 > From: Pius Padayatti <ppadaya...@gmail.com> > Subject: Fwd: [ccp4bb] Membrane Protein Crystallization Plates > > Hi board, > Although i do not want to endorse anything personally > earlier mail to Yuris response reflects my personal reflection of what i like. > > Here is a plate from Molecualr dimensions that i found > may be an alternate where you can chose the sandwich thickness > good idea but do not know what advantage it might have on > crystallization process. > > link: > http://www.moleculardimensions.com//shopdisplayproducts.asp?Search=Yes > > Thanks to Tony from molecular dimensions who point this out. > quote: > "We have many users of Laminex which offers a lot of flexibility > in that you can choose sandwich thickness as well as glass or plastic bases > and glass, plastic or film covers. > If you have not tested Laminex I would be pleased to send you a sample trial > pack. > > Tony Savill > Molecular Dimensions Inc." > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pius > Padayatti > Sent: 26 February 2012 01:08 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Membrane Protein Crystallization Plates > > Hi Yuri, > i strongly suggest these plates sold through Hampton research Paul > Marienfeld GmbH plates for your use. > here is a link , best plates in the market. > link: http://hamptonresearch.com/product_detail.aspx?cid=10&sid=182&pid=611 > > Plates comes with extra cover slips in addition to single glass cover for > four wells at a time whcih let you set these plates manually if you like it > that way. > > Good for automations as well. > only problem: since the galss is siliconized you can not write anything on > it (may be there is some industry grade marker might work.) But there is > enough place on side to stick a printed label or bar code for > your'automation for keeping records hope this is what you wanted to know. > > if you are money crunched and want to make some plates on your own. buy > regular micoscope slides, some two sided tapes (3M) very thin and a tool > that sold for cutting out small pieces of tissue samples. it looks like a > pen with sharp punch enough to make a hole in a 3M tape make a 27 hole plate > in a standard microslide. > > cheers > pius > > > > > > > On Sat, Feb 25, 2012 at 3:35 PM, Yuri Pompeu <yuri.pom...@ufl.edu> wrote: >> Hello Everyone, >> I am considering the purchase of crystallization plates for membrane > proteins. >> I would love to hear what some of the community thinks or has experienced > with these. >> Particulalrly the monoolein and monoolein/cholesterol coated plates ( >> I am not sure I can mention the vendor here but it "should" not matter) So > fire away. Is it worth it? Any succes stories? Bad experiences? >> I appreciate the input >> Best, >> Yuri > > > > -- > Pius S Padayatti,PhD, > Phone: 216-658-4528 > > > > -- > Pius S Padayatti,PhD, > Phone: 216-658-4528 > > ------------------------------ > > Date: Sun, 26 Feb 2012 21:52:29 +0100 > From: Jan Dohnalek <dohnalek...@gmail.com> > Subject: Postdoctoral position in structure-function studies of enzymes for > biotechnologies > > DEADLINE APPROACHING! > Our group has been involved in structural studies of several novel enzymes > interesting from the point of view of biotechnologies, > > such as Laccase from *S. coeliocolor, *beta-galactosidase from Arthrobacter > (660 kDa) or recently plant metal-dependent bifunctional nuclease or > bacterial organophosphate anhydrolases for removal of toxic warfare agents. To > continue studies in this area and apply mostly structure-driven analysis on > further targets we are still accepting applications for a postdoc position. > > The Institute of Macromolecular Chemistry of the Academy of Sciences (IMC) > in Prague, Czech Republic searches for highly motivated young researchers > for a full time research postdoctoral position in the area of *Structural > Analysis of Biomacromolecules.* > > > > The position is offered within the Department of Structural Analysis of > Biomacromolecules (http://www.imc.cas.cz/en/umch/o_struanal.html) where the > central technique is x-ray diffraction analysis of mostly protein > structures. > > > > *Topic A: Structure and function of enzymes for biotechnologies* > > *Structure-function studies of enzymes with biotechnological applications.* > > The work will be focused on defining macromolecular targets, protein > production and purification in collaboration with a partner, > crystallization, X-ray diffraction, determination and interpretation of > structure, design of mutations and complementary biophysical techniques, > including measurements of reaction kinetics, inhibition and complex > formation. The successful applicant will be also involved in ligand > selection/design and studies of complexes of such compounds with the target > macromolecules. > > The applicant has received PhD or equivalent in one of the following > fields: biophysics, physics, biochemistry, chemistry, molecular biology or > closely related. Required experience and skills: protein crystallography, > biochemistry, reaction kinetics, inhibition. Practical experience with > protein-ligand interaction studies (ITC, SPR, etc.) and with enzyme > modification/optimization is welcome. > > * * > The applicant has received PhD degree after May 28, 2008. > > *Contract type: * Full time, fixed term, 3 years, starting 1st > July 2012, EU funded via the Czech Ministry of Education. > > You can contact me on this e-mail address or send your full application > according to instructions available here: > > http://www.imc.cas.cz/en/umch/aktuality.htm?id=97 > > The deadline for full applications is February 29! > > Jan Dohnalek > > IMC Prague > > > > > -- > Jan Dohnalek, Ph.D > Institute of Macromolecular Chemistry > Academy of Sciences of the Czech Republic > Heyrovskeho nam. 2 > 16206 Praha 6 > Czech Republic > > Tel: +420 296 809 390 > Fax: +420 296 809 410 > > ------------------------------ > > Date: Sun, 26 Feb 2012 22:49:08 +0100 > From: "Bernhard C. Lohkamp" <bernh...@chem.gla.ac.uk> > Subject: Re: coot with probe and reduce > > Dear Raj, > > please follow exactly what is written in the FAQ > http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html#mozTocId860510. I > just updated it slightly to hopefully make things even clearer (*). You > seem to be mixing different possible setups. Either you move the files > to WinCoot\bin OR you specify them in other files. I assume you did all > of the above and got confused. > > Hope this helps, > > B > > (*) and there was a typo that the path separators have to be \\ rather > than \ (if you wish to specify the absolute file names). > >> Dear All, >> >> I am trying to use probe and reduce with coot new version. I tried as >> suggested in coot FAQ page- >> >> 1. renamed probe.exe and reduce.exe were put in C:\WinCoot\bin- didnt >> show validate/probe clashes as active n coot >> >> 2. made changes to group settings.py in wincoot/share/coot/python >> folder to >> probe_command = "C:\WinCoot\bin\probe.exe" >> reduce_command = "C:\WinCoot\bin\reduce.exe" >> probe_command = "probe" >> reduce_command = "reduce" >> >> Any help is appreciated. >> Thanks >> raj >> >> No virus found in this message. >> Checked by AVG - www.avg.com <http://www.avg.com> >> Version: 2012.0.1913 / Virus Database: 2114/4829 - Release Date: 02/24/12 >> > > ------------------------------ > > End of CCP4BB Digest - 25 Feb 2012 to 26 Feb 2012 (#2012-58) > ************************************************************ > >
