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. Th

Data contains personal data

Language

English

Method and outcome

Time period(s) investigated

2021-09 – 2022-03

Data format / data structure

Other

Species and taxons

Frankia

Data collection

Mode of collection: Web-based experiment
Description of the mode of collection: In silico protein modeling: we uploaded existing data, namely amino acid sequences, onto the SWISS-model portal. Here the software predicts the 3D structure of the protein. The data was then downloaded as .pdb files which can be used in special software to open and visualise the protein strucure.
Time period(s) for data collection: 2021-09 – 2022-03
Source of the data: Research data: Published, Research data

Geographic coverage

Geographic spread

Geographic description: The model organisms are occuring everywhere across the globe, and specified geographic location is therefore irrelevant. The dataset, description, and analyses are not impacted by geographical location.

Administrative information

Responsible department/unit

Department of Crop Production Ecology

Other research principals

Stockholm University

Funding 1

Funding agency: Swedish Research Council
Funding agency's reference number: VR2012-03061

Funding 2

Funding agency: Swedish Research Council
Funding agency's reference number: VR2019-05540

Topic and keywords

Research area

Bioinformatics (computational biology) (Standard för svensk indelning av forskningsämnen 2011)

Keywords

Carbon, Bacteria, Nitrogen, Bioinformatics, Protein modeling, Frankia

Publications

Berckx, F., Nguyen, TV., Hilker, R., Wibberg, D., Battenberg, K., Kalinowski, J., Berry, A., Pawlowski, K. (2024). Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2. Journal of Experimental Botany: erae446. https://doi.org/10.1093/jxb/erae446
DOI: https://doi.org/10.1093/jxb/erae446

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