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Re: [PyMOL] Symmetry Mates Problem
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From: humayun s. <hu...@gm...> - 2010-05-19 16:41:20
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Thank you all and certainly seems llike now I am going to some right direction. I have read some discussion part (page 14) of the paper Maia sent, as stated below, the BSA ( value for my dimer interfaces are ~1000 (as predicted by PISA) which according to the Krissinel paper, is biological relevant. Moreover, the hexameric structure is reported to exist in the same specie on which I am working on. It has been concluded in a number of studies [20, 68, 69, 70] that BSA larger than 600-850°A2 indicates a biologically relevant interface. A lower figure of 400 °A2 was found in Ref. [9] and then used in the Protein Quaternary Structure (PQS) server [5]. The minimal BSA of potentially stable crystal dimers in our dataset is found to be 390 °A2 (PDB entry 1SDX [67]), which agrees with the literature data. However, it follows from Figs. 3B,5A and above considerations that unspecific interactions may prevail at ABSA · 3000°A2, causing substantial changes to the original complexes, and, therefore, dimeric structures with low ABSA may be misrepresented by crystals. On Thu, May 20, 2010 at 1:29 AM, Maia Cherney <ch...@ua...> wrote: > In his latest paper > > > E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. > Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 > > Krissinel wrote that DGdiss error is 5kcal/mol. I think that DG~5kcal/mol > is a gray zone. Then he compares docking results with actual structures, a > lot of failures! Is your protein exactly the same as documented or from a > different species? My protein has three different oligomeric states from > three different species, and the monomers from different species superpose > well. > > Maia > > humayun scherrif wrote: > >> >> Thank you all for the replies. >> * The protein itself makes hexamer which is well documented and >> proved structural evidence from other cytoplasmic domains ( my >> structure is also a domain). * I have run PISA, but the online >> PISA server didnt give me output >> like standalone PISA in CCP4 (result is mentioned below). Online >> PISA results show that "there are not significant dimer >> interfaces and thus the trimer structure is because of only >> crystal packing result" >> * For homology modeling I didnt get any proper homologs which have >> hexameric assembly (I@ Bryn: I cant send you PDB id since its >> not submitted yet) >> >> Analysis of protein interfaces suggests that the following quaternary >> structures are stable in solution (I wonder the DGdiss is positive value, is >> it significant to make Hexamer assembly because I couldnt find any help to >> find out about the allowed values) >> >> ----.-----.---------------------------------------.--------------- >> Set | No | Size Id ASA BSA DGdiss | Formula >> ----+-----+---------------------------------------+--------------- >> 1 | 1 | 6 0 19917.7 5536.3 3.8 | A(2)B(2)C(2) >> ----+-----+---------------------------------------+--------------- >> 2 | 2 | 3 1 10722.9 2004.1 6.2 | ABC >> ----+-----+---------------------------------------+--------------- >> 3 | 3 | 4 2 14004.2 3014.9 0.5 | A(2)B(2) >> | 4 | 1 3 4217.5 0.0 -0.0 | A >> ----+-----+---------------------------------------+--------------- >> 4 | 5 | 2 4 7506.2 1003.3 7.0 | AB >> | 6 | 1 3 4217.5 0.0 -0.0 | A >> ----+-----+---------------------------------------+--------------- >> 5 | 7 | 2 5 7443.8 1000.8 6.8 | AB >> | 8 | 1 6 4282.4 0.0 -0.0 | A >> ----+-----+---------------------------------------+--------------- >> 6 | 9 | 2 7 7556.5 1008.3 2.0 | A(2) >> | 10 | 1 8 4227.1 0.0 -0.0 | A >> | 11 | 1 3 4217.5 0.0 -0.0 | A >> ----'-----'---------------------------------------'--------------- >> >> >> Waiting for your reply >> Thanks >> >> H >> >> >> >> >> On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick < >> rob...@ir... <mailto:rob...@ir...>> >> wrote: >> >> Also, if you would like to try homology modelling then that could >> work. However you would need a couple of hexamer strucutres to >> start with. It would probably take some tinkering with current >> tools. I would probably use an MD approach to solve this problem. >> Sorry I don't have a quick fix this is not my current area of >> expertise. >> Bryn >> >> Sent from my iPod >> >> On 19/05/2010, at 09:22, humayun scherrif <hu...@gm... >> <mailto:hu...@gm...>> wrote: >> >> >>> Thank you Bryn for your reply, But I have already tried all >>> possible symmetries that it generates, but it does not provide a >>> proper hexameric assembly. Does it mean this is due to problems >>> in crystal packing ? >>> Is there any alternative way to generate or by homology, which >>> server could be suitable ? >>> >>> Regards >>> >>> H >>> >>> >>> On Wed, May 19, 2010 at 4:02 PM, Robert Brynmor Fenwick >>> <rob...@ir... >>> <mailto:rob...@ir...>> wrote: >>> >>> There is a symmetry command that will build the crystal >>> symmetry from >>> the pdb header you could then delete the irrelevent molecules >>> to leave >>> the six that you want. >>> >>> Bryn >>> >>> If you have trouble with this I can hunt down the commands in >>> my labbook >>> >>> >>> > _______________________________________________ >>> > PyMOL-users mailing list (PyM...@li... >>> <mailto:PyM...@li...>) >>> >>> > Info Page: >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> > Archives: http://www.mail-archive.com/pymol- >>> > us...@li... >>> <mailto:us...@li...> >>> >>> >>> >>> >>> >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > -- Best Regards, Humayun Sharif Research Assistant Protein Structure and Function Laboratory Gwangju Institute Of Science & Technology, Gwangju, 500-712, Republic of Korea Tel (Res) :+82-62-718-4176 Tel (Lab) : +82-62-970-2549 Email: hu...@gm... |