Re: [ccp4bb] Symmetry Operations

[Eleanor Dodson]

you can fit your model chin A over chain B
First save chain A only to a new model  either in COOT or outside by editing
so now you have two Models - one A B C etc , and one only A
Calulat SSM. overlap or some such instruction of A over B  and change CHAIN
ID to X say
Now repeat with SSM overlap A to C.. etc

At end you can mere A with all copies..

But also maybe better to sort out the true symmetry first.
Do you have a suggested Space group or is it really P1?
Eleanor




On 23 August 2017 at 20:26, Lorenzo Briganti 
wrote:

> Dear Phenixbb and CCP4bb members,
>
>
> I'm currently refining a structure and facing some problems. It's
> originally a tetramer in solution, but I could only solve it in P1 group,
> with 8 molecules in the asymmetric unit (two tetramers). One of my chains
> is complete, but the others present some significant gaps. I believe I can
> use one chain and apply symmetry operations in order to produce a tetramer,
> I've heard it is possible using Coot, but I've never done that. Any
> suggestions?
>
>
> Best regards,
>
>
> Lorenzo
>

Re: [ccp4bb] Sugar-Pi-stacking

[Bärbel Blaum]

Hi Bernhard,

the interaction you are referring to is usually referred to as CH-pi  
interaction and not 'stacking', and that notation implies, as was  
pointed out, that the hydrophobic face of pyranose rings (most often  
GAL) is positioned such that the CH bond vectors interact with the  
aromatic orbitals. This interaction is a signature of lectin-glycan  
complexes - aromatic residues, especially tryptophan residues, are  
massively enriched in lectin binding sites. Despite the name the major  
energy gain of the apparant 'stacking' is, however, due to vdw  
interactions, with only about 0.5 kcal/mole contribution form the  
CH-pi interaction.


Regards from the ACS meeting Carb session :)

Bärbel

Zitat von Bernhard Rupp :


Thanks to all the respondents. Very useful links on a generally interesting
topic. I was pretty sure

that this is another case of imprecise notation/definition because even with
my limited QM I cannot see a

true pi-stacking in the sense of the narrow definition.



But, it seems to be frequently used in the context with sugarCH-aromatic
interaction, which is not good.



Much obliged, BR

  _

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp
[hofkristall...@gmail.com]
Sent: Wednesday, August 23, 2017 8:18 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Sugar-Pi-stacking

Hi Fellows,



there are some smart chemists amongst you, so I wonder - what precisely am I
to understand is

the nature of pi-stacking between an aromatic residue or (whatever
pi-orbital moiety) and a sugar moiety, disaccharide etc.?



Thanks for your help,



BR



--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org 

+1 925 209 7429

+43 767 571 0536

--

All models are wrong

but some are useful.

--



--
Bärbel Blaum, Ph.D.
Interfakultäres Institut für Biochemie (IFIB)
Hoppe-Seyler-Strasse 4
D-72076 Tübingen
Germany
+49 70 71 29 75 359

Re: [ccp4bb] Sugar-Pi-stacking

[Bernhard Rupp]

Thanks to all the respondents. Very useful links on a generally interesting
topic. I was pretty sure

that this is another case of imprecise notation/definition because even with
my limited QM I cannot see a

true pi-stacking in the sense of the narrow definition.  

 

But, it seems to be frequently used in the context with sugarCH-aromatic
interaction, which is not good.

 

Much obliged, BR

  _  

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp
[hofkristall...@gmail.com]
Sent: Wednesday, August 23, 2017 8:18 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] Sugar-Pi-stacking

Hi Fellows, 

 

there are some smart chemists amongst you, so I wonder - what precisely am I
to understand is

the nature of pi-stacking between an aromatic residue or (whatever
pi-orbital moiety) and a sugar moiety, disaccharide etc.?

 

Thanks for your help,

 

BR

 

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 767 571 0536

--

All models are wrong

but some are useful.

--

 

Re: [ccp4bb] A question about Cys and fluoro benzene ring

[Savvas Savvides]

Dear Cheng,

it is possible that the sulfhydryl of the cysteine might have reacted with the 
methyl fluoro benzyl group via nucleophilic aromatic substitution. Fluorine is 
not the best leaving group among the halides but it would certainly allow this 
especially if the ligand-protein incubation time was sufficient and if the the 
pH of the reaction is above 7. This would get the Cys-SH closer to the 
cysteinyl moiety (S:-). The pKa of the Cys-SH group is just under 8.5 and in 
your case it might even be lower depending on local structure environment, 
resulting in an even better nucleophile.

Your electron density indeed suggests that the sulfur from the Cys-SH is 
covalently bonded to the benzyl ring and this would happen at the carbon that 
originally carried the fluorine. You will have to remodel your ligand, keeping 
in mind that the fluorine will no longer be part of your ligand model. The 
methyl group will of course be retained.

It might also be useful to try to confirm the reactivity of the ligand of 
interest with the protein (reminiscent of a suicide or covalent inhibitor 
against cysteine proteases?) via some kind of an orthogonal method (e.g. mass 
spectrometry). This would even tell you if the particular cysteine in your 
structure is truly the relevant covalent target. In this way you can even 
compare washed and dissolved crystals of your protein-ligand complex with the 
complex in solution.

best wishes
Savvas


---
Savvas Savvides
VIB-UGent Center for Inflammation Research
Dept. Biochemistry & Microbiology, Ghent University
Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium
+32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: 
savvas.savvides_skype
http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx 





> On 23 Aug 2017, at 17:01, Cheng Zhang  wrote:
> 
> Hi everyone,
> 
> We recently got a structure of a receptor bound to a ligand. The ligand has a 
> fluoro methyl benzene ring moiety, which is close to a Cys residue in the 
> receptor. The density for the ligand and the Cys seems to suggest a covalent 
> bond. However, I don't know if a covalent bond is chemically possible. Also, 
> I believe Cys is rarely involved in cation-pi interactions? Any suggestions 
> for placing the Cys and the fluoro methyl benzene ring?
> 
> Thanks! 
> 
> Cheng
> 
> 
> 
> -- 
> -
> Cheng Zhang

[ccp4bb] Symmetry Operations

[Lorenzo Briganti]

Dear Phenixbb and CCP4bb members,


I'm currently refining a structure and facing some problems. It's originally a 
tetramer in solution, but I could only solve it in P1 group, with 8 molecules 
in the asymmetric unit (two tetramers). One of my chains is complete, but the 
others present some significant gaps. I believe I can use one chain and apply 
symmetry operations in order to produce a tetramer, I've heard it is possible 
using Coot, but I've never done that. Any suggestions?


Best regards,


Lorenzo

Re: [ccp4bb] Sugar-Pi-stacking

[Boaz Shaanan]

Hi Bernhard,


The aromatic-carbohydrate (the hydrophobic face of carbohydrate) was first reviewed in Weis and Drickamer 1996 review in Ann. Rev. Biochem. 65, 441-473 (see their Fig. 5). They didn't use the term Pi interaction though for the reason Ian mentioned I suppose.


Regards,


                Boaz



 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp [hofkristall...@gmail.com]
Sent: Wednesday, August 23, 2017 8:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Sugar-Pi-stacking





Hi Fellows, 
 
there are some smart chemists amongst you, so I wonder – what precisely am I to understand is
the nature of pi-stacking between an aromatic residue or (whatever pi-orbital moiety) and a sugar moiety, disaccharide etc.?
 
Thanks for your help,
 
BR
 
--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 767 571 0536
--
All models are wrong
but some are useful.
--
 

Re: [ccp4bb] Sugar-Pi-stacking

[Christian Roth]

Dear Bernhard,

the explanation can be found in here with additional references in.

J Am Chem Soc. 
2015 Dec 
9;137(48):15152-60. doi: 10.1021/jacs.5b08424. Epub 2015 Nov 30.



 Carbohydrate-Aromatic Interactions in Proteins.

Hope that will clarify the meaning.

Cheers

Christian



Am 23.08.2017 um 18:18 schrieb Bernhard Rupp:


Hi Fellows,

there are some smart chemists amongst you, so I wonder – what 
precisely am I to understand is


the nature of pi-stacking between an aromatic residue or (whatever 
pi-orbital moiety) and a sugar moiety, disaccharide etc.?


Thanks for your help,

BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org 

+1 925 209 7429

+43 767 571 0536

--

All models are wrong

but some are useful.

--

Re: [ccp4bb] Sugar-Pi-stacking

[Ian Tickle]

Hi Bernhard

Greetings!  I don't see how an aromatic-aliphatic interaction can be
classed as pi-stacking.  Surely it's just a normal dispersion interaction (
https://en.wikipedia.org/wiki/London_dispersion_force)?

Cheers

-- Ian


On 23 August 2017 at 18:18, Bernhard Rupp  wrote:

> Hi Fellows,
>
>
>
> there are some smart chemists amongst you, so I wonder – what precisely am
> I to understand is
>
> the nature of pi-stacking between an aromatic residue or (whatever
> pi-orbital moiety) and a sugar moiety, disaccharide etc.?
>
>
>
> Thanks for your help,
>
>
>
> BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> All models are wrong
>
> but some are useful.
>
> --
>
>
>

[ccp4bb] Sugar-Pi-stacking

[Bernhard Rupp]

Hi Fellows, 

 

there are some smart chemists amongst you, so I wonder - what precisely am I
to understand is

the nature of pi-stacking between an aromatic residue or (whatever
pi-orbital moiety) and a sugar moiety, disaccharide etc.?

 

Thanks for your help,

 

BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

All models are wrong

but some are useful.

--

 

[ccp4bb] Research Technician (Structural biology) position at SGC, University of Oxford

[Wyatt W. Yue]

Dear all,

We are advertising a research technician position in the Metabolism and
Organelle Biogenesis group at SGC University of Oxford, which processes a
variety of human medically-relevant proteins in recombinant expression
systems, and purifies the proteins for structural and biophysical studies.

Closing date: Wednesday 6th Sept 2017, 12pm UK


Interested candidates please apply via University of Oxford job page that
is accessible from here:

https://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/130724-Laboratory-Technician-Protein-Structural-Biology


Visit our SGC group page:

*http://www.thesgc.org/groupprofile/9491
*


Informal inquiries to:

wyatt@sgc.ox.ac.uk



-

Assoc Prof Wyatt W. Yue

Structural Genomics Consortium

Nuffield Department of Medicine

University of Oxford OX3 7DQ

+44 (0)1865 617757

http://www.thesgc.org/wyatt

[ccp4bb] Can not use system browser open external links (macOS Sierra)

[Wei Ding]

Dear all,
I hope to open a external links by double click the link in qtRView 1.16(ccp4 
log viewer), but no response,



and I check the preference, it seems ok.
My OS is "macOS Sierra,Version 10.12.6" and the CCP4 version is 7.0.0.36.


But that link can be open easily in Linux system with the same ccp4 version.

Dose anyone know what the problem is?
Waiting for your help.

Best!

--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: ding...@iphy.ac.cn