Re: [ccp4bb] A helix with leucine repeats

[R. Michael Garavito]

Dear Cheng,

Chris and Ruud have provided you with the typical interpretation of such a 
motif, but you have forgotten to give the CCP4 community the context of this 
leucine-repeat helix.  Is it amphipathic?  Does the protein also have 
transmembrane helices (as suggested by the figure provided) which would provide 
the membrane anchoring? 

Look up structurally similar membrane proteins (not necessarily homologous by 
sequence), such as proteins which have a monotonic-like membrane interaction, 
but that also have a transmembrane helix (monoamine oxidase or some mammalian 
cyt P450s).  If your protein is monotopic, look at that class of membrane 
proteins (squalene cyclase, fatty acid hydrolase, cyclooxygenase, etc.).  One 
structurally undescribed motif is a “reentrant membrane helix.”  In other 
words, look at context before assigning function.  

Good luck and hope this helps,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
513 Biochemistry Bldg.   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com




> On Mar 3, 2018, at 3:51 PM, Cheng Zhang  wrote:
> 
> Hi all,
> 
> We recently got a structure of a transmembrane protein. There is a helix that 
> is parallel to the membrane. The function of this helix is not known and we 
> are trying to make some hypothesis. A unique feature is that there are 
> repeated leucine residues on this helix facing the lipids. I am wondering if 
> anyone has seen a similar pattern and could suggest possible function, e.g. 
> membrane anchoring?
> 
> Thanks!
> 
> Best,
> 
> Cheng
> 
> 
> 
> 
> -- 
> -
> Cheng Zhang

Re: [ccp4bb] does 12 A diffraction worth optimization

[Mark J van Raaij]

it's always worth trying optimization, you never know.

also try to get a room-temperature diffraction image of your crystal, only then 
will you know if the cryo or freezing didn't damage it. If at RT it diffracts 
to high resolution, you will then know that you have to work on the 
cryo-conditions or on different mounting techniques 
(https://doi.org/10.1107/S0907444911031210 
).

RT diffraction can be done traditionally in a glass capillary, using a plastic 
capillary (like the Mitegen ones: 
https://www.mitegen.com/product/micrort-room-temperature-starter-kits/ 
), or 
in-plate, like described in this paper for instance: 
https://doi.org/10.1107/S0907444911023249 
.

Yet another option might be controlled dehydration: 
https://pubs.acs.org/doi/10.1021/cg500890r 
.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/


> On 3 Mar 2018, at 02:34, Natalia O  wrote:
> 
> Hello,
>  
> I got crystals of protein-nucleic acid complex, rod-shape, reproducible, 
> don’t visibly get damaged upon freezing; however they gave diffraction only 
> to about 12 A. I tried several crystals. My question is whether such crystals 
> worth optimization. Clearly a 4A diffracting crystal could potentially be 
> optimized to 3 – 2.5A, but if the diffraction that I am getting now is 12A it 
> could suggest that the system is so flexible that getting to 3A with this 
> crystal form is not possible at all. I just wonder if there is any statistics 
> or a rule of thumb about what initial diffraction worth optimization?
> 
> Thank you!
> -Natalia
> 

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

Re: [ccp4bb] validating a homlology model

[Ed Pozharski]

Assuming that your homology model is that of a dimer, you could put it in a 
large unit cell (just add CRYST1 record).  The only interface you will get from 
pisa will be your dimer interface.
If your homology model is a monomer, then pisa will not help, of course, and 
you would need to predict dimerization mode first. 


Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5

 Original message 
From: Careina Edgooms <02531c126adf-dmarc-requ...@jiscmail.ac.uk> 
Date: 3/2/18  6:44 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] validating a homlology model 

Dear all
What programs are best used for validate homology models? I know of molprobity 
but if there are no coordinates I cannot use it. Is there a way to use such 
programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface but again for 
homology model this cannot be done as there is no PDB model. Does anybody know 
way to use PISA software on my own model that is not deposited in PDB?
Thank you in advanceCareina

Re: [ccp4bb] does 12 A diffraction worth optimization

[Paul Miller]

Absolutely you should optimise! It's impossible to predict crystal behaviour. I 
had a 20 A crystal, and I set a new plate in the same reservoir with an 
additive screen and got a 3A crystal. It was probably a completely different 
crystal to be honest, lattice, etc, but one never knows, you just have to try. 
You can also try using the low res crystal as a seed. Plus a million other 
things.



Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN


 Original message 
>Date: Fri, 2 Mar 2018 17:34:18 -0800
>From: CCP4 bulletin board  (on behalf of Natalia O 
>)
>Subject: [ccp4bb] does 12 A diffraction worth optimization  
>To: CCP4BB@JISCMAIL.AC.UK
>
>   Hello,
>
>    
>
>   I got crystals of protein-nucleic acid complex,
>   rod-shape, reproducible, don’t visibly get damaged
>   upon freezing; however they gave diffraction only to
>   about 12 A. I tried several crystals. My question is
>   whether such crystals worth optimization. Clearly a
>   4A diffracting crystal could potentially be
>   optimized to 3 – 2.5A, but if the diffraction that
>   I am getting now is 12A it could suggest that the
>   system is so flexible that getting to 3A with this
>   crystal form is not possible at all. I just wonder
>   if there is any statistics or a rule of thumb about
>   what initial diffraction worth optimization?
>
>   Thank you!
>
>   -Natalia