[ccp4bb] Updated SAUC Cell Database

[Herbert J. Bernstein]

The SAUC Cell Database has been updated to 122596 PDB cells and 397452 COD
cells.  SAUC is accessible at

  http://iterate.sourceforge.net/sauc
or
  http://flops.arcib.org:8084/sauc/

The second link is to a faster machine, but with less network bandwidth

If you would like to install your own version locally, the source is
available in
the sauc.git repository iterate project at http://sf.net/projects/iterate at

 https://sourceforge.net/p/iterate/sauc/ci/master/tree/

or on github at

  https://github.com/yayahjb/sauc

  -- Herbert J. Bernstein
 yaya...@gmail.com

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

[Goldman, Adrian]

All true, I did my undergraduate thesis (at cambridge about 10**6 years ago it 
feels) on the formation of carboxylate-pairs in the gas phase….  But I agree 
with the thread: there is a metal there; it’s almost certainly not Mg, but it’s 
hard to say without further data whether its Mn, Fe, Cu, Zn - those being the 
most likely culprits.  Someone suggested that scanning the edges might tell, 
and I agree.  But what he might find is a mixture, as the metal is probably 
adventitious and has just been picked up, possibly from whatever is present in 
solution.  We’ve had that experience.

Adrian


On 29 Dec 2017, at 17:31, Tristan Croll 
> wrote:

In this case, yes - there’s clearly a metal ion coordinated there. But for the 
record, it is entirely possible (if somewhat rare) to get acidic side chains 
directly contacting each other. Look up “carboxyl-carboxylate pair”. They’re 
typically found at low pH and/or in quite protected environments. Think of it 
as having one carboxyl group protonated and H-bonding to the other, except that 
the proton is more-or-less equally shared. Their most common role is as 
pH-dependent conformational switches - very stably bonded below the pKa, 
wanting nothing to with each other above.



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY




On 29 Dec 2017, at 14:18, Robbie Joosten 
> wrote:

Hi Anurag,

There is a metal in the middle there. You need to figure out which one. Have a 
look at the crystallization conditions. If can also have a look at anomalous 
signal.

Cheers,
Robbie

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anurag 
Misra
Sent: Friday, December 29, 2017 14:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

Dear all,
I have solved a protein structure at 2.8 A resolution with Rfree 26%. In this 
structure catalytic His interacts with non catalytic Asp. This His-Asp pair 
(Chain A) is facing another identical His-Asp pair (in Chain B) which are 
related with 2-fold ncs (pics are attached) (The molecule exists as a dimer). 
There is another His-Asp pair in chain C (not shown in attached pic) which 
faces to the identical pair related to crystallographic 2-fold. (min distance 
Asp-Asp 2.58 A, His-His 3.6 A and His1-Asp1/His1-Asp2 ~3.0 A)
How to explain Asp-Asp head on pairs in close proximity? Is there a role of His 
in making such pairs. Is there any role of change in pKa to allow such 
interactions? Kindly suggest a few references where similar Asp-Asp pairs have 
been seen.

I appreciate your kind attention.
Thank you so much for helping me.
Best regards,
Anurag

Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

[Doug Juers]

Hi Yuvraj,

Here are some thoughts in addition to what's been suggested already:

1. A good recent reference is here: 
http://journals.iucr.org/f/issues/2015/06/00/en5564/index.html

2. The image you sent suggests cubic ice, indicating a higher glycerol 
concentration (maybe 35 or 40%) is needed. Also consider stepwise 
equilibrations.

3. Glycerol and ethylene glycol can increase protein solubility, so if the 
crystal cannot tolerate the higher glycerol concentration try some other 
classes of cryoprotective agents (e.g. sugars, methylamines (i.e. TMAO), 
alcohols, mixtures...see the above reference)


Best,
Doug

[ccp4bb] Les Houches/TSRC Workshop on Protein Dynamics, Chamonix Valley, May 27-June 1, 2018

[martin weik]

Dear colleague,

Registration is open for the Les Houches/TSRC Workshop on Protein 
Dynamics, to be held in Les Houches, close to Chamonix at the heart of 
the French Alps, from May 27 to June 1, 2018.


This international workshop is a forum for presenting and discussing 
results from state-of-the-art experimental approaches (including optical 
spectroscopy, NMR spectroscopy, X-ray crystallography, XFELs, electron 
microscopy, atomic-force microscopy and scattering methods), and 
theoretical and computational methods to studying protein dynamics.


The Les Houches – TSRC Protein Dynamics Workshop complements the 
long-standing TSRC Protein Dynamics Workshop, held every other year in 
the odd calendar years at the Telluride Science Research Center 
 in Telluride, Colorado. In Les 
Houches, about 30 invited speakers will give oral presentations that 
comprise a pedagogic introduction to the methodology employed, followed 
by applications from their own work. Each 30-minute presentation will be 
followed by 15 minutes of discussion. In addition to the 30 invited 
speakers, there will be space for 30 student/postdoctoral participants 
that can present posters.Itsrelatively small number of 
participantsfavorsexchangeof ideasacross disciplines and 
fosteringofcollaborations.A few slots for oral presentations are still 
available.


The Ecole de Physique des Houches can be conveniently reached from 
Geneva Airport(including the train station at the airport with direct 
connections to Zurich)by shuttle-bus service within 80 minutes .


Please find details of the program at :
https://www.sites.google.com/site/houches2018/

With best regards,

Martin Weik

--
Martin Weik, PhD
Structural Protein Dynamics Research Team
Institut de Biologie Structurale
CAMPUS EPN
71 avenue des Martyrs
CS10090
38044 Grenoble Cedex 9; France  

NEW Phone:(33) 4 57 42 85 80
NEW Fax:(33) 4 76 50 18 90  

email:  w...@ibs.fr
http://www.ibs.fr/groups/dynamics-and-kinetics-of-molecular/structural-protein-dynamics/?lang=en

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

[Tristan Croll]

In this case, yes - there’s clearly a metal ion coordinated there. But for the 
record, it is entirely possible (if somewhat rare) to get acidic side chains 
directly contacting each other. Look up “carboxyl-carboxylate pair”. They’re 
typically found at low pH and/or in quite protected environments. Think of it 
as having one carboxyl group protonated and H-bonding to the other, except that 
the proton is more-or-less equally shared. Their most common role is as 
pH-dependent conformational switches - very stably bonded below the pKa, 
wanting nothing to with each other above.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 29 Dec 2017, at 14:18, Robbie Joosten  wrote:
> 
> Hi Anurag,
>  
> There is a metal in the middle there. You need to figure out which one. Have 
> a look at the crystallization conditions. If can also have a look at 
> anomalous signal.
>  
> Cheers,
> Robbie
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anurag 
> Misra
> Sent: Friday, December 29, 2017 14:55
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance
>  
> Dear all,
> I have solved a protein structure at 2.8 A resolution with Rfree 26%. In this 
> structure catalytic His interacts with non catalytic Asp. This His-Asp pair 
> (Chain A) is facing another identical His-Asp pair (in Chain B) which are 
> related with 2-fold ncs (pics are attached) (The molecule exists as a dimer). 
> There is another His-Asp pair in chain C (not shown in attached pic) which 
> faces to the identical pair related to crystallographic 2-fold. (min distance 
> Asp-Asp 2.58 A, His-His 3.6 A and His1-Asp1/His1-Asp2 ~3.0 A)
> How to explain Asp-Asp head on pairs in close proximity? Is there a role of 
> His in making such pairs. Is there any role of change in pKa to allow such 
> interactions? Kindly suggest a few references where similar Asp-Asp pairs 
> have been seen.
>  
> I appreciate your kind attention.
> Thank you so much for helping me.
> Best regards,
> Anurag
>  
>  
> 

Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

[Kay Diederichs]

Hi Yuvaraj,

the importance of proper cryo mounting is under-appreciated in the community. 
Intensities of reflections on or close to ice rings cannot be recovered by the 
data processing software with good accuracy, which is detrimental for structure 
solution and refinement. Thus it is vital to avoid or at least minimize ice 
rings! 

Whenever I see real experts flash-freezing crystals and mounting them, I am 
impressed by their speed, diligence, and care for the details.  I get the 
impression that some labs educate students properly, whereas that knowledge is 
apparently not available in others.

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Cryo has some 
useful hints and references.
Unfortunately, I don't have a list of more recent publications which emphasize 
the details - others may fill this in.

An overview video is https://www.youtube.com/watch?v=FENUWRYXMOM - good music 
but no explanations. 
https://www.youtube.com/watch?v=QcsaWowulDM has explanations, and so has 
https://www.youtube.com/watch?v=yyY01zW_oaI . 

good luck,

Kay

On Thu, 28 Dec 2017 18:58:57 +0530, YUVARAJ I  wrote:

>Respected All,
> I have crystallized a protein. It is forming big crystals, I have checked
>in the home source,
>Without cryoprotectant - No diffraction (blank)
>with Ethylene glycol- No diffraction (blank)
>with PEG 3350 - 7A diffraction and No ice rings
> with Glycerol - 3.5A diffraction with ice rings
>
>I have tried soaking with glycerol different concentrations 10-30% glycerol
>from 30 secs to 5 min.
>No improvement in the diffraction quality.
>
>How to improve the diffraction quality of the crystals and avoid the big
>ice ring.
>
>I have attached the diffraction image with this mail.
>
>Thanks in advance for your valuable suggestions
>
>Regards
>Yuvaraj
>
>
>--
>

Re: [ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

[Eugene Osipov]

Hi, Yuvraj,
I can suggest two methods:
1) collect a dataset at room temperature
2)  crystallize your protein in cryoconditions. That is add 25 % of
glycerol to your crystallization conditions and perform small optimization
in terms of precipitant concentration.

2017-12-29 7:55 GMT+03:00 Prem Prakash :

>
> -- Forwarded message --
> From: Prem Prakash 
> Date: Fri, Dec 29, 2017 at 10:22 AM
> Subject: Re: [ccp4bb] how to improve the diffraction quality of the
> crystals and avoid icerings
> To: zaigham mahmood khan 
>
>
> Hi, Yuvraj
> Initially I also faced similar problems, then I tried various combinations
> of different additives in the crystallization drop. Then I got relatively
> good diffraction data (2.8 Angstrm) in 0.01mM Bacl2 (in my case). In my
> protein structure I can see the Ba2+ ion bound to the intersubunit
> junctions which probably results some extent of decreased degree of
> freedom. Of course you also need the optimization of cryoprotectant as well
> as I can see Glycerol is giving you good resolution compare to others.
>
> Good luck
> Prem
>
> On Fri, Dec 29, 2017 at 2:06 AM, zaigham mahmood khan <
> mahmood.zaig...@gmail.com> wrote:
>
>> Yuvraj
>>
>> This is a tough call. may be you need to look at this database:
>>
>> http://web.archive.org/web/20111011202903/http://idb.exst.ja
>> xa.jp/db_data/protein/search-e.php
>>
>> Importantly, when you click on "ex" for the tab, "cryoprotectant", a
>> window will pop up and you can read different kinds of cryoprotectants that
>> have been successfully attempted in the past. Off-course, this also depends
>> on type of precipitant that you used for crystallization. Apparently, this
>> seems as glycerol worked better in your case, may be because you have
>> salt-based precipitant.
>>
>>
>>
>> Best wishes
>>
>> -Z
>>
>>
>> Zaigham Mahmood Khan, PhD
>>
>> Icahn School of Medicine at Mount Sinai
>> Department of Oncological Sciences
>> 1470 Madison Avenue
>> 
>> New York
>> 
>>
>> On Thu, Dec 28, 2017 at 8:28 AM, YUVARAJ I  wrote:
>>
>>> Respected All,
>>>  I have crystallized a protein. It is forming big crystals, I have
>>> checked in the home source,
>>> Without cryoprotectant - No diffraction (blank)
>>> with Ethylene glycol- No diffraction (blank)
>>> with PEG 3350 - 7A diffraction and No ice rings
>>>  with Glycerol - 3.5A diffraction with ice rings
>>>
>>> I have tried soaking with glycerol different concentrations 10-30%
>>> glycerol from 30 secs to 5 min.
>>> No improvement in the diffraction quality.
>>>
>>> How to improve the diffraction quality of the crystals and avoid the big
>>> ice ring.
>>>
>>> I have attached the diffraction image with this mail.
>>>
>>> Thanks in advance for your valuable suggestions
>>>
>>> Regards
>>> Yuvaraj
>>>
>>>
>>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>


-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com