Re: [ccp4bb] non-symmetric tetramer ? 2nd round
No, constraints do not improved the Chis, but also don't harm them much. Which NSDs, from selection or superposition (damsel or damsup)? The superposition ones: >>> P1 egp1p_04-1.pdb !! Reference file egp1p_12-1r.pdb !! NSD = 0.912 egp1p_05-1r.pdb !! NSD = 0.900 egp1p_03-1r.pdb !! NSD = 0.960 egp1p_06-1r.pdb !! NSD = 0.878 egp1p_10-1r.pdb !! NSD = 1.016 egp1p_07-1r.pdb !! NSD = 0.876 egp1p_14-1r.pdb !! NSD = 1.014 egp1p_02-1r.pdb !! NSD = 0.995 egp1p_13-1r.pdb !! NSD = 1.037 egp1p_08-1r.pdb !! NSD = 1.004 egp1p_01-1r.pdb !! NSD = 1.100 egp1p_11-1r.pdb !! NSD = 1.067 egp1p_15-1r.pdb !! NSD = 1.021 egp1p_09-1r.pdb !! NSD = 0.969 >>> P2 egp2p_08-1.pdb !! Reference file egp2p_09-1r.pdb !! NSD = 0.927 egp2p_12-1r.pdb !! NSD = 1.024 egp2p_10-1r.pdb !! NSD = 1.024 egp2p_13-1r.pdb !! NSD = 1.056 egp2p_07-1r.pdb !! NSD = 0.884 egp2p_06-1r.pdb !! NSD = 0.884 egp2p_01-1r.pdb !! NSD = 0.869 egp2p_03-1r.pdb !! NSD = 1.256 egp2p_14-1r.pdb !! NSD = 0.836 egp2p_15-1r.pdb !! NSD = 0.836 egp2p_02-1r.pdb !! NSD = 1.318 egp2p_05-1r.pdb !! NSD = 1.168 egp2p_04-1r.pdb !! NSD = 1.168 >>> P222 egp22p01-1.pdb !! Reference file egp22p13-1r.pdb !! NSD = 1.268 egp22p14-1r.pdb !! NSD = 1.584 egp22p15-1r.pdb !! NSD = 1.584 egp22p02-1r.pdb !! NSD = 1.030 egp22p03-1r.pdb !! NSD = 1.030 egp22p07-1r.pdb !! NSD = 1.442 egp22p06-1r.pdb !! NSD = 1.442 egp22p04-1r.pdb !! NSD = 0.851 egp22p05-1r.pdb !! NSD = 0.851 egp22p08-1r.pdb !! NSD = 0.905 egp22p09-1r.pdb !! NSD = 0.905 egp22p12-1r.pdb !! NSD = 1.392 egp22p10-1r.pdb !! NSD = 1.392 >>> P4 egp4p_09-1.pdb !! Reference file egp4p_07-1r.pdb !! NSD = 0.923 egp4p_08-1r.pdb !! NSD = 0.923 egp4p_05-1r.pdb !! NSD = 0.886 egp4p_02-1r.pdb !! NSD = 0.861 egp4p_01-1r.pdb !! NSD = 0.861 egp4p_03-1r.pdb !! NSD = 0.998 egp4p_04-1r.pdb !! NSD = 0.998 egp4p_06-1r.pdb !! NSD = 1.176 egp4p_13-1r.pdb !! NSD = 1.079 egp4p_12-1r.pdb !! NSD = 1.079 egp4p_14-1r.pdb !! NSD = 0.868 egp4p_15-1r.pdb !! NSD = 0.868 egp4p_10-1r.pdb !! NSD = 1.309 egp4p_11-1r.pdb !! NSD = 1.309 >>>P5 egp5S206-1.pdb !! Reference file egp5S202-1r.pdb !! NSD = 0.675 egp5S205-1r.pdb !! NSD = 0.789 egp5S210-1r.pdb !! NSD = 1.044 egp5S212-1r.pdb !! NSD = 0.998 egp5S215-1r.pdb !! NSD = 0.929 egp5S204-1r.pdb !! NSD = 0.740 egp5S201-1r.pdb !! NSD = 1.077 egp5S211-1r.pdb !! NSD = 1.126 egp5S213-1r.pdb !! NSD = 0.773 egp5S209-1r.pdb !! NSD = 1.192 egp5S207-1r.pdb !! NSD = 1.213 egp5S214-1r.pdb !! NSD = 1.270 egp5S208-1r.pdb !! NSD = 0.710 Em 29-07-2010 13:11, Kushol Gupta escreveu: Fred, Two cents - I think the P1 SAXS solution should strongly guide your choice of symmetry constraint above all else in this case: do any of the symmetry-restrained shape reconstructions *improve* the statistics (chi) and stability of the shape (NSD) when compared to the P1 result? Also, it sounds like you have other data - do the theoretical Rs, f/fo, etc of the shapes generated agree well with your other measurements? Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 Of course, 222 has not a 4 axis,
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
So, that was my previous question. Em 29-07-2010 14:14, Phoebe Rice escreveu: You don't have to keep the same number of symmetrical contacts. Original message Date: Thu, 29 Jul 2010 14:13:56 -0300 From: Fred Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round To: CCP4BB@JISCMAIL.AC.UK Clarifying... That's happened because I was talking about the symmetry of the SAXS envelop/particle. I understand that if you consider the symmetry of the whole particle, say a tetramer of identical subunits, you can have the 4-fold axis when asking for 222 symmetry envelop, which gives you a 422 envelop. I disagree with you statement "there is no fundamental reason that a tetramer has to have any particular symmetry". Thinking only in the low resolution envelop, that's not true. Try to arrange 4 spheres in a non-symmetrical way keeping the same number of reciprocal contacts. Em 29-07-2010 13:17, Phoebe Rice escreveu: It sounds like you're missing something fundamental about 222 symmetry, but I may be misunderstanding you - there IS no fourfold. In fact, I think it is more common for the subunits within tetramers to be related to one another by three mutually perpendicular twofolds than a fourfold (e.g. the favorite classic hemoglobin has no fourfold anywhere). And there is no fundamental reason that a tetramer has to have any particular symmetry. Phoebe Original message Date: Thu, 29 Jul 2010 13:04:02 -0300 From: Fred Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round To: CCP4BB@JISCMAIL.AC.UK Of course, 222 has not a 4 axis, otherwise it would be a 4- fold axis. But that's the output of the program. P4 exp. model has a 4- fold axis along the longest axis, while the P222 MODEL has a 4-fold axis along the smallest, which doesn't make any sense. Can you imagine something build up with 4 identical subunits and 222 symmtry, but without a 4-fold axis at the molecular level (I mean at the envelop resolution level)? Em 29-07-2010 12:32, Vellieux Frederic escreveu: Hi, To quote you: "even my P222 experimental envelop does have a 4-fold axis" - this is not suprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nomenclature, these axes are named the P Q and R axes]. Fred. Fred wrote: Thanks all of you who promptly replied my question. I should have been more precise. I was referring to the symmetry of the tetrameric particle (point symmetry) at the molecular level not at the atomic level. This question has arisen because I have collected some SAXS data of my protein in solution and I don't have a molecular model to superpose to the experimental envelop. Others experimental data, gel filtration and NAT-PAGE, suggest a tetrameric particle. On the other side, P1, P2, P222 and P4 experimental envelops are quite different. So, I am not sure which symmetry to take. Considering the native state (no ligands at all), 4 identical subunits and that the interface of oligomarization have to be conserved, I would take P222 or P4. However, I can be able to imagine such spacial arrangement without a 4-fold axis at the molecular level. Indeed, even my P222 experimental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry& Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/0 1_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry& Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over f
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
Clarifying... That's happened because I was talking about the symmetry of the SAXS envelop/particle. I understand that if you consider the symmetry of the whole particle, say a tetramer of identical subunits, you can have the 4-fold axis when asking for 222 symmetry envelop, which gives you a 422 envelop. I disagree with you statement "there is no fundamental reason that a tetramer has to have any particular symmetry". Thinking only in the low resolution envelop, that's not true. Try to arrange 4 spheres in a non-symmetrical way keeping the same number of reciprocal contacts. Em 29-07-2010 13:17, Phoebe Rice escreveu: It sounds like you're missing something fundamental about 222 symmetry, but I may be misunderstanding you - there IS no fourfold. In fact, I think it is more common for the subunits within tetramers to be related to one another by three mutually perpendicular twofolds than a fourfold (e.g. the favorite classic hemoglobin has no fourfold anywhere). And there is no fundamental reason that a tetramer has to have any particular symmetry. Phoebe Original message Date: Thu, 29 Jul 2010 13:04:02 -0300 From: Fred Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round To: CCP4BB@JISCMAIL.AC.UK Of course, 222 has not a 4 axis, otherwise it would be a 4- fold axis. But that's the output of the program. P4 exp. model has a 4- fold axis along the longest axis, while the P222 MODEL has a 4-fold axis along the smallest, which doesn't make any sense. Can you imagine something build up with 4 identical subunits and 222 symmtry, but without a 4-fold axis at the molecular level (I mean at the envelop resolution level)? Em 29-07-2010 12:32, Vellieux Frederic escreveu: Hi, To quote you: "even my P222 experimental envelop does have a 4-fold axis" - this is not suprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nomenclature, these axes are named the P Q and R axes]. Fred. Fred wrote: Thanks all of you who promptly replied my question. I should have been more precise. I was referring to the symmetry of the tetrameric particle (point symmetry) at the molecular level not at the atomic level. This question has arisen because I have collected some SAXS data of my protein in solution and I don't have a molecular model to superpose to the experimental envelop. Others experimental data, gel filtration and NAT-PAGE, suggest a tetrameric particle. On the other side, P1, P2, P222 and P4 experimental envelops are quite different. So, I am not sure which symmetry to take. Considering the native state (no ligands at all), 4 identical subunits and that the interface of oligomarization have to be conserved, I would take P222 or P4. However, I can be able to imagine such spacial arrangement without a 4-fold axis at the molecular level. Indeed, even my P222 experimental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry& Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
Fred, Two cents - I think the P1 SAXS solution should strongly guide your choice of symmetry constraint above all else in this case: do any of the symmetry-restrained shape reconstructions *improve* the statistics (chi) and stability of the shape (NSD) when compared to the P1 result? Also, it sounds like you have other data - do the theoretical Rs, f/fo, etc of the shapes generated agree well with your other measurements? Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 Of course, 222 has not a 4 axis, otherwise it would be a 4-fold axis. But that's the output of the program. P4 exp. model has a 4-fold axis along the longest axis, while the P222 MODEL has a 4-fold axis along the smallest, which doesn't make any sense. Can you imagine something build up with 4 identical subunits and 222 symmtry, but without a 4-fold axis at the molecular level (I mean at the envelop resolution level)? Em 29-07-2010 12:32, Vellieux Frederic escreveu: > Hi, > > To quote you: "even my P222 experimental envelop does have a 4-fold > axis" - this is not suprising, a particle with 222 symmetry does not > have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes > that intersect at the origin (of the "particle", of the molecule) [and > for the nomenclature, these axes are named the P Q and R axes]. > > Fred. > > Fred wrote: >> Thanks all of you who promptly replied my question. >> I should have been more precise. I was referring to the symmetry of >> the tetrameric particle (point symmetry) at the molecular level not >> at the atomic level. This question has arisen because I have >> collected some SAXS data of my protein in solution and I don't have a >> molecular model to superpose to the experimental envelop. Others >> experimental data, gel filtration and NAT-PAGE, suggest a tetrameric >> particle. On the other side, P1, P2, P222 and P4 experimental >> envelops are quite different. So, I am not sure which symmetry to >> take. Considering the native state (no ligands at all), 4 identical >> subunits and that the interface of oligomarization have to be >> conserved, I would take P222 or P4. However, I can be able to imagine >> such spacial arrangement without a 4-fold axis at the molecular >> level. Indeed, even my P222 experimental envelop does have a 4-fold >> axis. >> I appreciate if you could add some more comments on this. >> Thanks in advance, >> Fred > >
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
Of course, 222 has not a 4 axis, otherwise it would be a 4-fold axis. But that's the output of the program. P4 exp. model has a 4-fold axis along the longest axis, while the P222 MODEL has a 4-fold axis along the smallest, which doesn't make any sense. Can you imagine something build up with 4 identical subunits and 222 symmtry, but without a 4-fold axis at the molecular level (I mean at the envelop resolution level)? Em 29-07-2010 12:32, Vellieux Frederic escreveu: Hi, To quote you: "even my P222 experimental envelop does have a 4-fold axis" - this is not suprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nomenclature, these axes are named the P Q and R axes]. Fred. Fred wrote: Thanks all of you who promptly replied my question. I should have been more precise. I was referring to the symmetry of the tetrameric particle (point symmetry) at the molecular level not at the atomic level. This question has arisen because I have collected some SAXS data of my protein in solution and I don't have a molecular model to superpose to the experimental envelop. Others experimental data, gel filtration and NAT-PAGE, suggest a tetrameric particle. On the other side, P1, P2, P222 and P4 experimental envelops are quite different. So, I am not sure which symmetry to take. Considering the native state (no ligands at all), 4 identical subunits and that the interface of oligomarization have to be conserved, I would take P222 or P4. However, I can be able to imagine such spacial arrangement without a 4-fold axis at the molecular level. Indeed, even my P222 experimental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
Hi, To quote you: "even my P222 experimental envelop does have a 4-fold axis" - this is not suprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nomenclature, these axes are named the P Q and R axes]. Fred. Fred wrote: Thanks all of you who promptly replied my question. I should have been more precise. I was referring to the symmetry of the tetrameric particle (point symmetry) at the molecular level not at the atomic level. This question has arisen because I have collected some SAXS data of my protein in solution and I don't have a molecular model to superpose to the experimental envelop. Others experimental data, gel filtration and NAT-PAGE, suggest a tetrameric particle. On the other side, P1, P2, P222 and P4 experimental envelops are quite different. So, I am not sure which symmetry to take. Considering the native state (no ligands at all), 4 identical subunits and that the interface of oligomarization have to be conserved, I would take P222 or P4. However, I can be able to imagine such spacial arrangement without a 4-fold axis at the molecular level. Indeed, even my P222 experimental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred
Re: [ccp4bb] non-symmetric tetramer ? 2nd round
Thanks all of you who promptly replied my question. I should have been more precise. I was referring to the symmetry of the tetrameric particle (point symmetry) at the molecular level not at the atomic level. This question has arisen because I have collected some SAXS data of my protein in solution and I don't have a molecular model to superpose to the experimental envelop. Others experimental data, gel filtration and NAT-PAGE, suggest a tetrameric particle. On the other side, P1, P2, P222 and P4 experimental envelops are quite different. So, I am not sure which symmetry to take. Considering the native state (no ligands at all), 4 identical subunits and that the interface of oligomarization have to be conserved, I would take P222 or P4. However, I can be able to imagine such spacial arrangement without a 4-fold axis at the molecular level. Indeed, even my P222 experimental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred On Wed, 28 Jul 2010 15:31:45 -0300 Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb
Re: [ccp4bb] non-symmetric tetramer ?
Here is another example of a tetramer with neither 222 or 4 fold symmetry: http://www.ncbi.nlm.nih.gov/pubmed/7792597 Thierry -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Vellieux Frederic Sent: Thursday, July 29, 2010 03:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] non-symmetric tetramer ? Non-symmetric tetramers: you can check out Tete-Favier et al (1993), Acta Cryst. D49, 246: the quaternary structure was assumed to have local 222 symmetry. It turned out this was not exactly the case: the actual symmetry of the object (the molecule) was "pseudo" 2t2t2t. So in addition to 2-fold axes being common as an assembly mechanism (leading to the quite common 222 symmetry) you can have deviations from this symmetry. Fred. Fred wrote: > Dear CCP4bb, > Could someone please, point me to some references about non-symmetric > tetramers? If I have a tetramer composed by 4 identical subunits, > it'll always have a P4 point group symmetry? > Thank in advance, > Tomb > > * This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete.
Re: [ccp4bb] non-symmetric tetramer ?
Peanut lectin, when we solved the structure in the 90's, had a very unusual non-symmetric tetramer. Till we solved the structure, there were examples only of symmetric tetramers 222 (say, ConA), or 4 (e.g. Neuraminadase) in the literature. Peanut lectin had two dimers, each with a two-fold symmetry, but the two dimers were not related by mutually perpendicular two-fold axes (PNAS, 1994, vol 91, 227- 231). Shekhar On Thu, Jul 29, 2010 at 1:05 PM, Vellieux Frederic wrote: > Non-symmetric tetramers: you can check out Tete-Favier et al (1993), Acta > Cryst. D49, 246: the quaternary structure was assumed to have local 222 > symmetry. It turned out this was not exactly the case: the actual symmetry > of the object (the molecule) was "pseudo" 2t2t2t. So in addition to 2-fold > axes being common as an assembly mechanism (leading to the quite common 222 > symmetry) you can have deviations from this symmetry. > > Fred. > > Fred wrote: > >> Dear CCP4bb, >> Could someone please, point me to some references about non-symmetric >> tetramers? If I have a tetramer composed by 4 identical subunits, it'll >> always have a P4 point group symmetry? >> Thank in advance, >> Tomb >> >> >> -- Shekhar C. Mande Centre for DNA Fingerprinting and Diagnostics Bldg.7, Gruhakalpa 5-4-399/B, Nampally Hyderabad- 51 INDIA Phone: +91-40-24749401 Fax: +91-40-24749448
Re: [ccp4bb] non-symmetric tetramer ?
Thurs., July 29th 2010 EBI moreover.. the protein Andrew has suggested was determined several around Goto http://www.ebi.ac.uk/pdbe/ enter the uniprot P00362 in the middle box "Retrieve PDB entries using an external database identifier " (check UniProt) and you get a more complete list. click on an entry, and from its atlas page you can get the Quaternary structure Miri On Thu, 29 Jul 2010, Miri Hirshberg wrote: Thurs., July 29th 2010 EBI Morning, I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD) DOI10.1016/0022-2836(88)90130-1 Miri On Wed, 28 Jul 2010, A Leslie wrote: Hi Fred, If your tetramer show negative cooperativity between the 4 sites for ligand binding, then it is possible to get a tetramer with (say) only one subunit occupied by ligand, which can introduce considerable asymmetry if ligand binding gives rise to a hinge type closure of two domains around the ligand site. An example of this is glyceraldehyde 3-phosphate dehydrogenase which has been solved with one, two (and possibly 3) NADs bound per tetramer. I'm afraid you will need to do a literature search to find the references, but AJ Wonacott will be one of the authors. Cheers Andrew On 28 Jul 2010, at 19:31, Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb
Re: [ccp4bb] non-symmetric tetramer ?
Thurs., July 29th 2010 EBI Morning, I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD) DOI10.1016/0022-2836(88)90130-1 Miri On Wed, 28 Jul 2010, A Leslie wrote: Hi Fred, If your tetramer show negative cooperativity between the 4 sites for ligand binding, then it is possible to get a tetramer with (say) only one subunit occupied by ligand, which can introduce considerable asymmetry if ligand binding gives rise to a hinge type closure of two domains around the ligand site. An example of this is glyceraldehyde 3-phosphate dehydrogenase which has been solved with one, two (and possibly 3) NADs bound per tetramer. I'm afraid you will need to do a literature search to find the references, but AJ Wonacott will be one of the authors. Cheers Andrew On 28 Jul 2010, at 19:31, Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb
Re: [ccp4bb] non-symmetric tetramer ?
Hi Fred, If your tetramer show negative cooperativity between the 4 sites for ligand binding, then it is possible to get a tetramer with (say) only one subunit occupied by ligand, which can introduce considerable asymmetry if ligand binding gives rise to a hinge type closure of two domains around the ligand site. An example of this is glyceraldehyde 3-phosphate dehydrogenase which has been solved with one, two (and possibly 3) NADs bound per tetramer. I'm afraid you will need to do a literature search to find the references, but AJ Wonacott will be one of the authors. Cheers Andrew On 28 Jul 2010, at 19:31, Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non- symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb
Re: [ccp4bb] non-symmetric tetramer ?
Non-symmetric tetramers: you can check out Tete-Favier et al (1993), Acta Cryst. D49, 246: the quaternary structure was assumed to have local 222 symmetry. It turned out this was not exactly the case: the actual symmetry of the object (the molecule) was "pseudo" 2t2t2t. So in addition to 2-fold axes being common as an assembly mechanism (leading to the quite common 222 symmetry) you can have deviations from this symmetry. Fred. Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb
Re: [ccp4bb] non-symmetric tetramer ?
Dear Tomb, if your tetramer (oligomer in general) is part of the asymmetric unit the crystal's space group can be independent from the tetramer. Tim On Wed, Jul 28, 2010 at 03:31:45PM -0300, Fred wrote: > Dear CCP4bb, > Could someone please, point me to some references about non-symmetric > tetramers? If I have a tetramer composed by 4 identical subunits, it'll > always have a P4 point group symmetry? > Thank in advance, > Tomb -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] non-symmetric tetramer ?
The symmetry of a homotetramer will depend (in part) on how many types of interfaces it has. Some sort of 2-fold symmetry is probably more likely. Crystallization unit cell is another matter, and depends on contact interfaces. We study a protein that is a homotetramer that has two different dimer interfaces (a "dimerization" and a "tetramerization" interface) giving a biological unit with multiple 2-fold axes. So far, it will crystallize in unit cells C2, a "double-size" C2 on c, C222(1), P4(1)2(1)2, P6(5), P3(2), and I2(1)2(1)2(1) depending on the variant and ligands bound. My students seem extra-talented in generating new unit cells and space groups of the same protein for us to puzzle out via MR. Cheers. On 7/28/2010 2:31 PM, Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] non-symmetric tetramer ?
I had a tetramer with 222 symmetry--1f38 and related entries. Is that what you mean? Jacob - Original Message - From: "Fred" To: Sent: Wednesday, July 28, 2010 1:31 PM Subject: [ccp4bb] non-symmetric tetramer ? Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb *** 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 ***
