Re: [ccp4bb] Beamline Scientist position at Diamond Light Source

[Hall, Dave (DLSLtd,RAL,LSCI)]

Hi

I would like to remind you the closing date for applications for this Beamline 
Scientist post at Diamond is this coming Sunday (6th August).

Best wishes

Dave

From: Hall, Dave (DLSLtd,RAL,LSCI) 
Date: Thursday, 20 July 2023 at 09:14
To: ccp4bb 
Subject: Beamline Scientist position at Diamond Light Source
Hi Everyone

We have a permanent opening for people interested in a beamline scientist role 
to join the MX group at Diamond:

https://vacancies.diamond.ac.uk/vacancy/mx-group-beamline-scientist-530029.html

Closing date for applications is 6th August.

Feel free to contact me for further information.

Best wishes

Dave
--
MX Group Leader
Diamond Light Source
www.diamond.ac.uk/mx



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[ccp4bb] wwPDB News: Updated Annotation and Standardization of Peptide Residues

[Deborah Harrus]

Dear all,

In October 2023, the wwPDB will roll out updated Chemical Component 
Dictionary (CCD) data files with standardized atom naming and additional 
annotation of protein backbone and terminal atoms within peptide 
residues. Entries containing those updated CCDs will also be updated 
accordingly. This will improve the Findability and Interoperability of 
the PDB data, as well as open up new opportunities to use the updated 
peptide residue annotation.


As part of this remediation process, we will add new data items to the 
CCD files for peptide-linking components to label atoms that form the 
backbone, N- or C-terminal groups. Three new CCD data items will be 
added to the CCD category _chem_comp_atom as pdbx_backbone_flag, 
pdbx_n-terminal_flag and pdbx_c-terminal_flag, flagging the backbone, 
N-terminal and C-terminal atoms, respectively.


Furthermore, we will be standardizing the atom nomenclature of peptide 
backbone atoms in CCD files to follow a standard convention. This will 
follow a set of rules, outlined in the documentation linked below, 
ensuring that atom nomenclature for carboxyl groups, amino groups and 
side chain linked carbons (C-alpha) follow a standard atom nomenclature. 
This will allow clear identification of backbone atoms for peptide 
residues across the whole archive.


Detailed information about this work is available from the wwPDB 
website, including PDBx/mmCIF dictionary extension and example files 
(GitHub ; Peptide Residues 
Chemical Component Dictionary Remediation Documentation 
).


Updated peptide CCDs will have standardized atom names and backbone / 
N- and C- terminal annotation./

/
/Updated peptide CCDs will have standardized atom names and backbone / 
N- and C- terminal annotation./


We encourage developers of software packages for refinement or 
visualization of PDB data to review this information.


Questions or feedback? Contact deposit-h...@mail.wwpdb.org.

The peptide residues chemical component dictionary remediation project 
is part of the protein chemical modifications (PCMs) and post 
translational modifications (PTMs) remediation project, a wwPDB 
collaborative project carried out principally by PDBe at EMBL-EBI, and 
is funded by BBSRC grant number BB/V018779/1.


Read this news online: 
https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687


Kind regards,

Deborah Harrus

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] 3D-Beacons update: Search for structural models by protein sequence

[David Armstrong]

Dear ccp4bb,

The 3D-Beacons resource has undergone some major improvements, including 
updates to the API and a new sequence search feature.



The 3D-Beacons Network, originally announced in September 2021 
, 
brings together experimentally determined and predicted protein 
structure models, alongside relevant quality metrics, from several 
providers and makes them freely available in one place. The data are 
provided by a number of services, including the Protein Data Bank in 
Europe (PDBe), AlphaFold DB, SWISS-MODEL, Protein Ensemble Database 
(PED), Small Angle Scattering Biological Data Bank (SASBDB), Genome3D, 
and PDBe Knowledge Base (PDBe-KB). 3D-Beacons allows users to search 
using UniProt accession and access protein structure models from all 
these different providers in a standardised format.



The 3D-Beacons resource has been updated to include some major 
improvements to the infrastructure and the public website 
(3d-beacons.org ). This includes an update to 
the API to support POST queries to the summary endpoint, up to a maximum 
of 10 accessions. The release also includes a brand new sequence search 
feature, allowing users to easily find relevant structures based on an 
input protein sequence.


For more information, view the full news item at 
https://www.ebi.ac.uk/pdbe/news/3d-beacons-update-search-structural-models-protein-sequence 
Kind Regards, David


--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK



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[ccp4bb] Connecting DNA between asymmetric units?

[Ronnie Berntsson]

Hi all,

We have recently solved a structure of a DNA binding protein in complex with 
DNA to ca 2.5 Å. The space group is P212121 and contains 3 protein molecules in 
the asymmetric unit (current Rwork/Rfree = 20.4/24.1). The protein was 
crystallized together with a 60 bases long poly-A oligo (ssDNA). Each protein 
molecule binds to a stretch of this DNA. However, only 15 bp of the DNA is part 
of the asymmetric unit, with each protein molecule binding 5 bp. The DNA then 
goes on to the next ASU (with its 3 proteins) and so forth. There is no 
sequence specificity to the DNA, so it can “slide”. Redoing the structure in P1 
does not really help, as due to its “sliding” nature the density is still 
continuous in between ASUs.

Currently, the structure model thus consists of 3 protein molecules and one 15 
bases long DNA. However, the density for the DNA is as I wrote continuous into 
the neighboring ASUs. Any advice for how to deal with this in the model would 
be most welcome! We can of course explain it in the manuscript that we’ll 
submit, but would feel good if one can represent it in a better way also in the 
pdb. Hopefully I’ve managed to convey my question here, but let me know if any 
clarification is needed.

Best wishes,
Ronnie

--
Ronnie Berntsson, PhD
Chair of the Young Academy of Sweden

Department of Medical Biochemistry and Biophysics, Umeå University
90187 Umeå, Sweden
e-mail: ronnie.bernts...@umu.se
phone: +46 90 7865235
web: https://www.biostruct.umu.se/principal-investigators/ronnie-berntsson/



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