Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

[Andrew Leslie]

Dear Jacob,

Citrate synthase is another early (historically) case, and GAPDH (on binding 
NAD). 

Andrew

On 27 Feb 2014, at 19:43, "Keller, Jacob"  wrote:

> Dear Crystallographers,
> 
> Does anyone know of good examples of large, reversible conformational changes 
> occurring between ligand-free and -bound states? Could also be a non-relevant 
> molecule binding, like sulfate or something inducing dubiously -relevant 
> changes. I already know of the calmodulin and periplasmic binding protein 
> families, but does anyone know of others out there?
> 
> All the best,
> 
> Jacob Keller
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Farms Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

[Avinash Punekar]

Dear Jacob,

We recently solved crystal structures of apo and ligand bound forms of a 
cofactor S-adenosyl-methionine (SAM) dependent methyltransferase RlmJ 
(http://nar.oxfordjournals.org/content/41/20/9537.long). Comparison of the 
structures revealed that binding of the cofactor and a substrate analogue 
adenosine monophosphate (AMP) to RlmJ induces major structural rearrangements 
in the four loop regions surrounding the active site. The N-terminal tail 
undergoes a large movement (88 deg rotation) to cover the cofactor binding site 
and a neighboring loop region transforms into an α-helix.

Avinash

-- 
Avinash S. Punekar
 
Department of Cell and Molecular Biology
Uppsala University

Re: [ccp4bb] unusually low B-factors

[Eleanor Dodson]

I think it may well be a problem with the scaling.
It is hard to get a reasonable estimate of the Wilson B at 3A -
especially in a small cell.
Look at the Log Graph plots - one associated with R factor gives you
 and  v resolution. They SHOULD overlap pretty well, but
sometimes they dont and sometimes that is because the OVERALL B is
badly estimated.
Of course it is a function of the data but often hard to correct..
Eleanor


On 27 February 2014 16:26, Paul Paukstelis  wrote:
> Greetings,
>
> We've been working on a number of related structures. Crystals are in P64
> with fairly small unit cell (40,40,55) and only diffract to around 2.5-3.0,
> so we aren't working with a lot of reflections. For several of these data
> sets the maps look very reasonable but Refmac refinement gives us unusually
> low B-factors after either individual or grouped refinement (average of
> around 10 A2 with some residues around 2 A2) while others are more 'normal'
> (avg. 30-40) with very similar maps. I suspect something in data processing,
> but I was wondering if there are opinions about what I should look for in
> cases like this. Thanks in advance.
>
> --paul

[ccp4bb] Biophysics faculty position at Milwaukee

[George Sheldrick]

Abbas Ourmazd who is physics professor at Milwaukee has asked me to post 
this job advert on CCP4bb:

http://jobs.sciencecareers.org/job/325225/assistant-or-associate-professor-in-biophysics/

George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

[ccp4bb] CCP4-6.4.0 Update 009

[Ville Uski]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes:

* areaimol
- Fix to atom records of output pdb.
* mrbump
- Several fixes including bug fixes to allow SHELXE to run when
  submitting jobs to a cluster.
* theseus
- Theseus now distributed with CCP4 for use in AMPLE.
* spicker
- Spicker now distributed with CCP4 for use in AMPLE.
* feckless
- A new auxiliary program for the forthcoming multi-lattice version
  of imosflm.
* ample
- Fix for NMR re-modelling option and Scwrl can be run as an
  additional step.
* freerflag
- Fixed non-equal subsets for different free-R-flag values when the
  COMPLETE keyword is used. Updated the documentation.

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

Ville
-- 
Scanned by iCritical.

[ccp4bb] Postdoctoral Scholar position in Structural Biology

[Oleg Tsodikov]

A Postdoctoral Scholar position in structural biology is available in the
laboratory of Dr. Oleg Tsodikov at the Department of Pharmaceutical
Sciences at the University of Kentucky (
http://pharmacy.mc.uky.edu/faculty/tsodikov/index.php),
starting immediately to study oncogenic transcription factors and their
interactions with DNA, other proteins and small molecule ligands. We seek
highly motivated individuals with a Ph.D. degree and with experience in
X-ray crystallography.

Applicants should email Dr. Tsodikov at
oleg.tsodi...@uky.edu.
Please, include a CV and contact information for 3 references.


-- 
Oleg Tsodikov, Ph.D.
Associate Professor of Pharmaceutical Sciences
University of Kentucky College of Pharmacy
Department of Pharmaceutical Sciences
BioPharm Bldg, Room 425
789 S. Limestone
Lexington, KY 40536

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

[Elizabeth Goldsmith]

Jacob,

Many enzymes do this, not quite as dramatic as calmodulin, but especially 
hexokinase, and this is important because it was the origin of Koshland's 
"induced fit" idea.  Glycogen phosphorylase, aspartate transcarbamylase, and 
phosphofructokinase also do radical things involving subunit rearrangements.

On Feb 28, 2014, at 2:49 AM, Andrew Leslie wrote:

> Dear Jacob,
> 
> Citrate synthase is another early (historically) case, and GAPDH (on binding 
> NAD). 
> 
> Andrew
> 
> On 27 Feb 2014, at 19:43, "Keller, Jacob"  wrote:
> 
>> Dear Crystallographers,
>> 
>> Does anyone know of good examples of large, reversible conformational 
>> changes occurring between ligand-free and -bound states? Could also be a 
>> non-relevant molecule binding, like sulfate or something inducing dubiously 
>> -relevant changes. I already know of the calmodulin and periplasmic binding 
>> protein families, but does anyone know of others out there?
>> 
>> All the best,
>> 
>> Jacob Keller
>> 
>> ***
>> Jacob Pearson Keller, PhD
>> Looger Lab/HHMI Janelia Farms Research Campus
>> 19700 Helix Dr, Ashburn, VA 20147
>> email: kell...@janelia.hhmi.org
>> ***

Elizabeth Goldsmith
Patti Bell Brown (Chilton) Professor 
Department of Biophysics
214 645 6376 
be...@chop.swmed.edu

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

[william Kennedy]

Dear CCP4 community -

In case anyone missed this, one interesting example of large conformational
changes associated with ligand binding event(s) is T7 RNA polymerase,
involved in the initiation, elongation and termination of mRNA synthesis
following promoter recognition.

Tom Steitz' review from 2004 [The structural basis of the transition from
initiation to elongation phases of transcription, as well as translocation
and strand separation, by T7 RNA polymerase. Curr Opin Struct
Biol.14(1):4-9] is a good entry point for background information, although
there is a large body of work from many biochemists and structural
biologists that continues to this day.

PDB ID Codes:
'apo'-enzyme:  1aro
promoter binary complex: 1cez
transcribing complex: 1gln
Elongation complex with major conformational change: 1msw
Intermediate transcribing complex: 3e3j.

This is not meant to be an exhaustive list of what is available in the
literature or the PDB, but may whet your curiosity.


Wm. Kennedy
Sr. Med. Dir.
Genenetech





On Fri, Feb 28, 2014 at 12:49 AM, Andrew Leslie wrote:

> Dear Jacob,
>
> Citrate synthase is another early (historically) case, and GAPDH (on
> binding NAD).
>
> Andrew
>
> On 27 Feb 2014, at 19:43, "Keller, Jacob" 
> wrote:
>
> > Dear Crystallographers,
> >
> > Does anyone know of good examples of large, reversible conformational
> changes occurring between ligand-free and -bound states? Could also be a
> non-relevant molecule binding, like sulfate or something inducing dubiously
> -relevant changes. I already know of the calmodulin and periplasmic binding
> protein families, but does anyone know of others out there?
> >
> > All the best,
> >
> > Jacob Keller
> >
> > ***
> > Jacob Pearson Keller, PhD
> > Looger Lab/HHMI Janelia Farms Research Campus
> > 19700 Helix Dr, Ashburn, VA 20147
> > email: kell...@janelia.hhmi.org
> > ***
>

[ccp4bb] >> Scientist or Research Assistant Professor position in Shanghai

[thomas.earnest]

Scientist or Research Assistant Professor

A scientist or research assistant professor position (depending on experience 
and qualifications) is available to develop intelligent software for advanced 
protein crystallography experiments at the Shanghai synchrotron in 
collaboration with ShanghaiTech University. This position will include the 
development of data processing and analysis, beamline control, and data 
collection software as part of a multi-institutional team. The ability to 
understand the complex system of instrumentation and its scientific 
applications are critical.

Requirements:
Many years experience in programing in C++, Python, Java, Tck/Tk, and other 
languages used in scientific applications and modern instrument control 
systems., as demonstrated by record of productivity. Experience in EPICS will 
be a plus. Experience in machine learning and artificial intelligence as 
applied to instrument control also a large plus. Experience in protein 
crystallography is a plus. Ability to communicate well in English is required 
and conversational Mandarin would be beneficial.

Contact Thomas Earnest at  
thomas.earn...@sinap.ac.cn for details.

[ccp4bb] Full programme for the Eighth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, April 10-12 2014, Hamburg

[Elspeth Garman]

The Eighth International Workshop on X-ray Radiation Damage to Biological 
Crystalline Samples will be held at the EMBL and DESY, Hamburg, Germany  from 
April 10th (13:00) to April 12th (13:00) 2014.

The full programme for this Workshop can now be found at: 
http://www.rd-eight.org/RD8-01/programme/index.html

On-line registration for this Workshop is open at:
http://www.rd-eight.org/

Registration is Euro 150 before 15th March and Euro 180 after 15th March.
All registration is through the on-line site.

Due to the generosity of our partners and sponsors 
(http://www.rd-eight.org/RD8-01/sponsorship/index.html), we are able to offer 5 
Bursaries of E150 each to PhD students who would like to attend the Workshop 
and bring posters.
Please contact Elspeth Garman (elspeth.gar...@bioch.ox.ac.uk) before 13th March 
if you would like to apply for one of these, and include a supporting letter 
from your supervisor. 

This series of workshops was originally concerned with the effects of radiation 
damage during investigation of protein structures by X-ray crystallography. 
Other techniques of structural biology are now being included to ensure greater 
information exchange. The workshop will therefore be of interest to all those 
using ionising radiation to examine biological structures at the molecular 
level.
It will consist of around 25 talks of 20-25 minutes each, with slots allocated 
for discussion. 

The sessions will cover:

Session 1 Basic Understanding of Radiation Damage Mechanisms 
Session 2 Practical Aspects of Reducing Radiation Damage 
Session 3 Biological studies affected by Radiation Damage 
Session 4 Damage at New Sources - XFEL and new synchrotrons 
Session 5 Radiation Damage in Complementary Fields 
Session 6 Additional Aspects of Radiation Damage 

Abstract submission will close on March 15th.

The organizers are: Elspeth Garman, Martin Weik, Gleb Bourenkov, Henry Chapman, 
Alke Meents, Sean McSweeney, Colin Nave, Arwen Pearson, Raimond Ravelli, Gerd 
Rosenbaum, Thomas Schneider and Soichi Wakatsuki.
---


  Professor Elspeth F. Garman,
  Director of Systems Biology Programme, Doctoral Training Centre
  Tutor for Graduates, Brasenose College Postal address:
  Laboratory of Molecular Biophysics,
  Department of Biochemistry,
  University of Oxford,  Tel: (44)-1865-613297
  South Parks Road,  FAX: (44)-1865-613201
  OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk 
www.bioch.ox.ac.uk/garmangroup
--
The University of Oxford's Doctoral Training Centre has three available 
programmes for October 2014 entry: Life Sciences Interface Doctoral Training 
Centre, Systems Biology Doctoral Training Centre and Systems Approaches to 
Biomedical Science Industrial Doctorate Centre.
To find out more, visit: http://www.dtc.ox.ac.uk/