Data for: "Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2"

Abstract

The datafiles contain protein model structures as .pdb file format (Protein Data Bank) for the enzyme "2-oxoglutarate dehydrogenase/decarboxylase" of different Frankia species, in relation to the publication. These protein models were generated in silico on SWISS-Model website, using the crystal structure of Mycobacterium smegmatis (reference A0R2B1) and Staphylococcus epidermis (reference Q5HPC6) are templates. The modeling was performed using standard parameters, as described by the website instructions. The input data, namely amino acid sequences, were pulled from The National Center for Biotechnology Information (NCBI, Genbank) using a pBLAST search to identify the amino acid sequence from different Frankia species. The corresponding references to find these sequences are available as documentation files and in the supplementary data of the associated manuscript on the journal website. Each of the .pdb files contains information of one Frankia species, and is named after the corresponding species. For example, the datafile Falni refers to the model built for the protein of Frankia alni. These .pdb files are made available for those wishing to verify our conclusions. We recommend using protein visuallisation software, such as ChimeraX to open and visualise the data. The visualisation of the models are given in the supplementary figures.

Keywords

Carbon; Bacteria; Nitrogen; Bioinformatics; Protein modeling; Frankia

Published in

Publisher: Swedish National Data Service

SLU Authors

• Berckx, Fede

  • Department of Crop Production Ecology, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Bioinformatics (Computational Biology)

Publication identifier

• DOI: https://doi.org/10.5878/wxkv-s592

Permanent link to this page (URI)

https://res.slu.se/id/publ/139389