Re: [ccp4bb] extra density between inter-chain cysteine

[CHAVAS Leonard]

When running non-denaturing gel (SDS-gel without reducing agent should work), 
do you see a dimer? Same question during your sample preparation, if you are 
performing anything like SEC. If you do have DTT in lysis buffer, that could 
do. If nothing as such anywhere, honestly no idea...

Cheers, leo


> On 21 Mar 2016, at 15:09, Manjula Ramu  wrote:
> 
> I had no reducing agent in my protein buffer as wel as in crystal condition. 
> I have only sodium citrate in the condition.
> 
> On Mar 21, 2016 6:54 PM, "CHAVAS Leonard" 
>  wrote:
> DTT perhaps?
> 
> Cheers, leo
> 
> > On 21 Mar 2016, at 14:04, Pedro Matias  wrote:
> >
> > Does it make sense to consider 2 extra S-atoms bridging the 2 cysteines? 
> > What would be the bond distances? What is the meaning of the red e.d. in 
> > the 2nd figure?
> >
> > Às 12:44 de 21/03/2016, Eleanor Dodson escreveu:
> >> No idea, but it is a lovely map.
> >>
> >> Are you sure the residue is CYS? You could check the anom map to see if 
> >> the S give a signal.
> >> Eleanor
> >>
> >> On 20 March 2016 at 04:36, Manjula Ramu  wrote:
> >> Dear community,
> >>
> >> I have got a crystal structure of 16Kda protein, which was solved at 1.9 
> >> A. Protein crystallised in dimer form and I could observe a continuous 
> >> extra density between cysteine of  two chains. Distance between two 
> >> intermolecular cysteine is 7.8 A.  Please help me to interpret this extra 
> >> density. Thanks in advance.
> >>  I have attached the screen shots of the map.
> >>
> >>
> >> Thanks and Regards,
> >> Manjula R
> >> Research Scholar
> >> Department of Biophysics
> >> National Institute of Mental Health and Neurosciences
> >> Bengaluru-29, Karnataka
> >> INDIA
> >> E-mail: manjula@gmail.com
> >> Mobile no:+91-9538553356
> >> http://www.nimhans.kar.nic.in/
> >>
> >>
> >>
> >>
> >
> >
> > --
> >
> > Industry and Medicine Applied Crystallography
> > Macromolecular Crystallography Unit
> > ___
> > Phones : (351-21) 446-9100 Ext. 1669
> >  (351-21) 446-9669 (direct)
> >  Fax   : (351-21) 441-1277 or 443-3644
> >
> > email :
> > mat...@itqb.unl.pt
> >
> >
> >
> > http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> > http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> >
> >
> > Mailing address :
> > Instituto de Tecnologia Quimica e Biologica
> > Universidade Nova de Lisboa
> > Av. da República - EAN
> > 2780-157 Oeiras
> > PORTUGAL
> >
> > ITQB, a great choice for your PhD
> >
> > https://youtu.be/de6j-aaTWNQ
> >
> >
> > Master Programme in Biochemistry for Health
> >
> > https://youtu.be/UKstDCFjYI8
> 
> -
> Leonard Chavas
> -
> Synchrotron SOLEIL
> Proxima-I
> L'Orme des Merisiers
> Saint-Aubin - BP 48
> 91192 Gif-sur-Yvette Cedex
> France
> -
> Phone:  +33 169 359 746
> Mobile: +33 644 321 614
> E-mail: leonard.cha...@synchrotron-soleil.fr
> -
> 

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

Re: [ccp4bb] extra density between inter-chain cysteine

[CHAVAS Leonard]

DTT perhaps?

Cheers, leo

> On 21 Mar 2016, at 14:04, Pedro Matias  wrote:
> 
> Does it make sense to consider 2 extra S-atoms bridging the 2 cysteines? What 
> would be the bond distances? What is the meaning of the red e.d. in the 2nd 
> figure?
> 
> Às 12:44 de 21/03/2016, Eleanor Dodson escreveu:
>> No idea, but it is a lovely map.
>> 
>> Are you sure the residue is CYS? You could check the anom map to see if the 
>> S give a signal.
>> Eleanor
>> 
>> On 20 March 2016 at 04:36, Manjula Ramu  wrote:
>> Dear community,
>> 
>> I have got a crystal structure of 16Kda protein, which was solved at 1.9 A. 
>> Protein crystallised in dimer form and I could observe a continuous extra 
>> density between cysteine of  two chains. Distance between two intermolecular 
>> cysteine is 7.8 A.  Please help me to interpret this extra density. Thanks 
>> in advance.
>>  I have attached the screen shots of the map.
>> 
>> 
>> Thanks and Regards,
>> Manjula R 
>> Research Scholar
>> Department of Biophysics 
>> National Institute of Mental Health and Neurosciences
>> Bengaluru-29, Karnataka
>> INDIA
>> E-mail: manjula@gmail.com
>> Mobile no:+91-9538553356
>> http://www.nimhans.kar.nic.in/
>> 
>> 
>> 
>> 
> 
> 
> -- 
> 
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
> 
> email : 
> mat...@itqb.unl.pt
> 
> 
> 
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
> 
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Universidade Nova de Lisboa
> Av. da República - EAN
> 2780-157 Oeiras
> PORTUGAL
> 
> ITQB, a great choice for your PhD
> 
> https://youtu.be/de6j-aaTWNQ
> 
> 
> Master Programme in Biochemistry for Health
> 
> https://youtu.be/UKstDCFjYI8

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-