Re: [ccp4bb] Serine
lovely density - i would like to know what % of series have multiple conformations - it would need a survey I guess of PDB depositions, not just coordinates, but checking maps.. Eleanor On 21 May 2012 22:21, Uma Ratu rosiso2...@gmail.com wrote: Thank you All for you inputs. Uma On Mon, May 21, 2012 at 5:06 PM, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu wrote: Yes, as Jacob says, alternative conformation of the serine. Quite common. Bert -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu [rosiso2...@gmail.com] *Sent:* Monday, May 21, 2012 4:57 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Serine Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma
Re: [ccp4bb] Serine
Dear Uma 1. The protein sequence given in the databases, do from time to time have errors, particularly if you are working with old proteins (when the sequencing was done a long time ago). What you observe could also be a threonine or even a valine. You should check whether homologous protein also have a serine on that position. I Normally do not assign double conformation unless you have fairly high resolution data, it is a bit hard to judge what the resolution is here. Often a double conformation is accompanied with negative difference density on top of the assigned atom, if you lower the sigma level a little, you often see it. 2. It is also common to have local frameshift errors in loop regions, even in reasonable high resolution data. I think you should double check the region to make sure you are not facing this problem, it is surprisingly difficult to detect sometimes, but you will know when you got the right. Cheers Preben On 5/21/12 10:57 PM, Uma Ratu wrote: Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma -- J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: j.p.mo...@ncmm.uio.no Tel: +47 2284 0794 http://www.jpmorth.dk
Re: [ccp4bb] Serine
3. Of course if you are working on recombinant protein, you should double check the sequencing results from the cloning Preben On 5/21/12 11:21 PM, Uma Ratu wrote: Thank you All for you inputs. Uma On Mon, May 21, 2012 at 5:06 PM, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu mailto:lambertus.vandenb...@umassmed.edu wrote: Yes, as Jacob says, alternative conformation of the serine. Quite common. Bert *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu [rosiso2...@gmail.com mailto:rosiso2...@gmail.com] *Sent:* Monday, May 21, 2012 4:57 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Serine Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma -- J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: j.p.mo...@ncmm.uio.no Tel: +47 2284 0794 http://www.jpmorth.dk
Re: [ccp4bb] Serine
I believe that's an alternative conformationtry modeling as such and see what happens. Jacob On Mon, May 21, 2012 at 3:57 PM, Uma Ratu rosiso2...@gmail.com wrote: Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Serine
Yes, as Jacob says, alternative conformation of the serine. Quite common. Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu [rosiso2...@gmail.com] Sent: Monday, May 21, 2012 4:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Serine Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma
Re: [ccp4bb] Serine
Thank you All for you inputs. Uma On Mon, May 21, 2012 at 5:06 PM, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu wrote: Yes, as Jacob says, alternative conformation of the serine. Quite common. Bert -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu [rosiso2...@gmail.com] *Sent:* Monday, May 21, 2012 4:57 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Serine Dear All: Some of serine residues in my model have extra positive Fo-Fc density at the edge of side chain. Some don't have. It is not like from phosphates. I am wondered what is the cause for these extra density. Could these serines be post-translational modified? I have the images attached. P289ser-0512-1 does not have the extra green, where P140ser-0512-1 has. Thank you for you advice and comment Uma
