[ccp4bb] Please Respond to the RCSB PDB User Survey and Raffle

[Christine Zardecki]

RCSB PDB is running an online survey to help us better understand 
RCSB.org and PDB-101 users and interests.

People who submit their responses at https://www.surveymonkey.com/r/RLRGRXX
can also enter into a drawing for a poster, 2018 calendar, or Zika model.

All users are encouraged to respond.

Thanks in advance for your consideration!

Christine

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Re: [ccp4bb] Adding unnatural amino acid

[Paul Emsley]

On 17/10/2017 17:49, Rashi Aggarwal wrote:

Dear all,

I am trying to add an unnatural amino acid to a structure in coot. I was able to successfully place the 
residue in the electron density. Also, I could establish links between the residue and the polypeptide chain 
using the 'make links' option in coot.


However, I was wondering how to establish covalent bonds between the unnatural amino acid and other residues 
in the peptide chain. Any advice will be appreciated




Make sure that the "group" of your ligand is L-peptide.

Paul

[ccp4bb] Adding unnatural amino acid

[Rashi Aggarwal]

Dear all,

I am trying to add an unnatural amino acid to a structure in coot. I was
able to successfully place the residue in the electron density. Also, I
could establish links between the residue and the polypeptide chain using
the 'make links' option in coot.

However, I was wondering how to establish covalent bonds between the
unnatural amino acid and other residues in the peptide chain. Any advice
will be appreciated

Thanks

Best,
Rashi

[ccp4bb] Structural Biology Postdoctoral Position

[Wai-Hong Tham]

https://www.wehi.edu.au/research-officer-infection-immunity-division

An opportunity exists for a Research Officer to join the Infection and Immunity 
Division at the Walter and Eliza Hall Institute to study the molecular events 
that occur during malaria parasite entry into human red blood cells.

This is a postdoctoral position for a researcher with structural biology 
experience. The position is available for 3 years in the first instance. Salary 
range ranging from $86,472 - $92,817 and is dependent on qualifications and 
experience.

Application deadline is October 20th 2017. To apply, please follow the link 
above. For additional questions, please contact A/Prof. Wai-Hong Tham at 
t...@wehi.edu.au.

[ccp4bb] Postdoctoral positions available

[Barondeau, David P]

Dear all,

   We are looking to fill postdoctoral positions in my lab.  See below.

Postdoctoral positions in the Barondeau lab at Texas A University Department 
of Chemistry are available immediately for highly motivated, creative 
individuals with a strong interest in biophysical and/or bioinorganic 
chemistry. Our labs are located in the Interdisciplinary Life Sciences building 
(http://vpr.tamu.edu/resources/ilsb), where we have access to state-of-the-art 
facilities for structural biology, mass spectrometry, and enzymology.

Our group is focused on understanding metallocofactor assembly and the 
functional tuning partnership between metallocofactors and their protein 
environments.

Project 1.  Structure-function studies of the human Fe-S assembly complex. This 
project combines recombinant DNA methods with enzymology, chemical biology, and 
structural methods and is funded by the NIH (renewed in 2017). We recently 
reported crystal and EM structures along with functional properties of the 
mitochondrial cysteine desulfurase (NFS1-ISD11-ACP) complex 
(https://www.ncbi.nlm.nih.gov/pubmed/28634302).
Highlights of our study:

  *   http://www.science.tamu.edu/news/story.php?story_ID=1812#.WUlPlmjyuUl
  *   
https://f1000.com/prime/article?articleId=727738370_medium=email_source=ts
  *   
https://www-ssrl.slac.stanford.edu/content/science/highlight/2017-09-30/structure-human-cysteine-desulfurase-complex

We report lock-and-key or anchoring interactions between the acyl-chain of ACP 
and ISD11 (a member of the eukaryotic-specific LYRM protein superfamily) along 
with a novel cysteine desulfurase architecture. This core cysteine desulfurase 
complex also binds three additional proteins, including the Friedreich's ataxia 
protein frataxin, to generate the fully functional Fe-S cluster assembly 
complex. Our objectives are to elucidate structural properties for how these 
additional proteins bind to the core complex and provide mechanistic details of 
how allosteric protein interactions, lipid binding, and post-translational 
modifications modulate Fe-S cluster biosynthesis.

Project 2. Fluorophore labeling and kinetic interrogation of Fe-S assembly 
pathways. This project (funded by the NSF) combines chemical biology, 
fluorescent plate reader and circular dichroism based assays and global fit 
kinetic analysis to elucidate the function of proteins in bacterial Fe-S 
assembly and transfer pathways. We have previously reported an intein-based 
approach to fluorophore label Fe-S proteins with rhodamine and then use 
fluorescence to monitor cluster content. This approach has the advantage of 
only monitoring Fe-S clusters bound to the protein or protein complex that is 
labeled with the fluorophore. For additional information see 
http://pubs.acs.org/doi/10.1021/ja510998s and 
http://pubs.acs.org/doi/abs/10.1021/acschembio.6b00632. Our objectives are to 
test the proposed roles of iron donor, activator/inhibitor, chaperone, 
intermediate carrier and cluster conversion proteins as well as evaluate 
kinetic vs thermodynamic control in transfer and regulatory pathways.

Contact Dr. David Barondeau (barond...@tamu.edu) for 
additional details.
To apply for a position, please submit a brief description of research 
interests, career goals, CV, and contact information for three references.



-
David P. Barondeau
Associate Professor
Department of Chemistry
Texas A University
301 Old College Main
College Station, TX 77843
Office: ILSB 1196A
Phone: (979) 458-0735
http://www.chem.tamu.edu/rgroup/barondeau/

[ccp4bb] Travel bursaries to CCP4 Study Weekend 2018 - deadline for applications 31st October 2017

[Karen McIntyre]

TRAVEL BURSARIES

Limited funds have been made available to help pay travel costs for students 
and young post-docs from non-UK laboratories.

Please send a separate letter, signed by your supervisor and stating the 
expected cost of travel in pounds sterling, to justify applications for travel 
support. Supervisors are asked to nominate only one candidate from their 
Laboratory.

Delegates are expected to travel by the most economic means possible.

Candidates from less favoured regions will be given preference.

Applications should be sent to:

Helen Walker
CCP4 Study Weekend Travel Bursary
Science and Technology Facilities Council
Rutherford Appleton Laboratory
RCaH 1.22
Harwell Oxford
Didcot
OX11 0FA, UK

You can also fax copies of your letters to Helen on +44 (0)1235 567720 or 
e-mail ccp4_study_week...@stfc.ac.uk .

Applications for Travel Assistance MUST be received by 31 October 2017.

Regards

Karen McIntyre
CCP4 Study Weekend Local Organising Committee
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

[*] @ccp4_mx

[cid:image002.png@01D34736.25FD26F0]

**Please note that I only work part-time until 1.30pm**

Re: [ccp4bb] exclude water from anisotropic refinement in PDB_REDO

[Robbie Joosten]

Hi Abhishek,

At the moment, there isn't. However, the decision to use anisotropic B-factors 
is based on comparing the refinement a fully isotropic model with that of a 
fully anisotropic model using the Hamilton test. So it should be safe to use 
anisotropic B-factors for all atoms.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Abhishek Anan
> Sent: Monday, October 16, 2017 19:12
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] exclude water from anisotropic refinement in PDB_REDO
> 
> Hi all,
> 
> Is there a way to exclude water from anisotropic refinement in PDB_REDO?
> 
> 
> Best regards,
> 
> 
> Abhishek