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Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Peptide on two-fold axis - was: PEG molecule crossing a two-fold crystallographic symmetry axis From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Date: 2009-05-04 Dear Li Defeng, From the original Email, I had the impression that the peptide was not part of the protein (e.g.activation peptide, substrate). If it is part of your protein you have a problem. If a peptide superimposes with its symmetry-mate (like you have), the maximum occupancy is 0.5 whatever you do. Some options which come to my mind: -the peptide is lost in half of your molecules e.g. due to protelytic degragdation. This can easily be checked by running a gel of protein from your crystal -half of the peptides is disordered and therefore not visible. You might want to very carefully examine the electron density maps if you see any signs of this. However, even if you do not find out what is the cause, you have no choice but to refine the peptide with 0.5 occupancy. Best regards, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of lidefeng Sent: Friday, May 01, 2009 2:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis Dear Herman.Schreuder, Perhaps there is some misunderstanding about my question. There is one molecule in the asymmetric unit (showed as symbos A). After the 2nd crystallographic symmetric operation, another molecule appears (symbol B). However, the density show that there is one peptide chain cross the 2nd axis (symbol C). If we give chain C occupancy of 0.5, only 50% of chain C belongs to molecules A and B, respectively. In another word, , it looks like one half of chain C belongs to molecule A and the other belongs to B. It means that one half of chain C belongs to molecule A disappear, so do that belongs to molecule B. 2nd axis AAAAAA BBBBBB AAAAAA BBBBBB AA BB / CCCCCCC CCCCCCC Your sincerely De-Feng Li lidefeng@moon.ibp.ac.cn 2009-05-01 Defeng Li, Dr., Email: lidefeng@moon.ibp.ac.cn National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China ======= 2009-04-30 14:52:00 You writed in your letter：======= >Dear Feng-Li, > >The other half occupancy peptide is generated by crystallographic symmetry (the twofold), you need only to build one. To check that everything fits properly, you should switch on the crystallographic symmetry in coot. (Draw -> Cell & Symmetry). > >Good luck! >Herman > > >-----Original Message----- >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >lidefeng >Sent: Thursday, April 30, 2009 3:44 AM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG >molecule crossing a two-fold crystallographic symmetry axis > >Dear Tim Gruene, > > But how to illustrate the other one half occupancy of peptide? Disorder ? > > > Your sincerely > De-Feng Li > lidefeng@moon.ibp.ac.cn > 2009-04-30 > >Defeng Li, Dr., >Email: lidefeng@moon.ibp.ac.cn >National Laboratory of Biomacromolecules, Institute of Biophysics, >Chinese Academy of Sciences, >15 Datun Road, Chaoyang District, >Beijing 100101, China > > >======= 2009-04-29 10:55:00 You writed in your letter：======= > >>Hello De-Feng Li, >> >>first of all sorry for changing the subject: I think starting a new >>thread from an existing one may hamper people who are going to search >>the archives in the future, therefore it is good practice to give it >>its separate subject line, even though it certainly is be very closely >>related. >> >>In your case you can refine two peptides each with an occupancy of >>0.5, one for each direction. >> >>Tim >>-- >>Tim Gruene >>Institut fuer anorganische Chemie >>Tammannstr. 4 >>D-37077 Goettingen >> >>GPG Key ID = A46BEE1A >> >> >>On Wed, 29 Apr 2009, lidefeng wrote: >> >>> Hi everyone, >>> >>> Following Chandrika's question, what should I do if one peptide chain crosses a two-fold crystallographic symmetry axis? >>> The peptide is not symmetric and the sidechain of one Se-Met (two after CS operation) is determined and conformed by MAD. >>> >>> Your sincerely >>> ????????De-Feng Li >>> ????????lidefeng@moon.ibp.ac.cn >>> ??????????2009-04-29 >>> >>> Defeng Li, Dr., >>> Email: lidefeng@moon.ibp.ac.cn >>> National Laboratory of Biomacromolecules, Institute of Biophysics, >>> Chinese Academy of Sciences, >>> 15 Datun Road, Chaoyang District, >>> Beijing 100101, China >>> >>> >>> ======= 2009-04-29 17:02:00 You writed in your letter?======= >>> >>>> Hello everyone, >>>> >>>> My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve : >>>> >>>> First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? >>>> >>>> Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ? >>>> >>>> Thanks, >>>> Chandrika >>> >>> ======================================================== >>> >>> > >======================================================== > ======================================================== CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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