Dataset for "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase"
A packaged software for use in salt bridge analysis in protein stability and rigidity. Reads in a hydrogenated and uniquely atomically numbered pdb file and provides constraint files "cov.in" "hbonds.in" and "hphobes.in" - for use with the FIRST softwares rigidity analysis suite - that correctly handle salt bridges and strong polar interactions within the structure.
Also included are the hydrogenated and formatted pdb files of a variety of thermophilic citrate synthase structures as used in the work for the publication "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase" by this dataset's authors.
Cite this dataset as:
Mcmanus, T.,
Wells, S.,
2019.
Dataset for "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase".
Bath: University of Bath Research Data Archive.
Available from: https://doi.org/10.15125/BATH-00566.
Export
Data
1a59.pdb
text/plain (487kB)
Creative Commons: Attribution 4.0
1a59.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
1aj8.pdb
text/plain (1MB)
Creative Commons: Attribution 4.0
1aj8.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
1iom.pdb
text/plain (507kB)
Creative Commons: Attribution 4.0
1iom.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
1ixe.pdb
text/plain (1MB)
Creative Commons: Attribution 4.0
1ixe.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
1o7x.pdb
text/plain (1MB)
Creative Commons: Attribution 4.0
1o7x.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
2c6x.pdb
text/plain (1MB)
Creative Commons: Attribution 4.0
2c6x.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
2cts.pdb
text/plain (594kB)
Creative Commons: Attribution 4.0
2cts.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
2ibp.pdb
text/plain (1MB)
Creative Commons: Attribution 4.0
2ibp.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
2ifc.pdb
text/plain (2MB)
Creative Commons: Attribution 4.0
2ifc.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
2r9e.pdb
text/plain (2MB)
Creative Commons: Attribution 4.0
2r9e.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
3enj.pdb
text/plain (621kB)
Creative Commons: Attribution 4.0
3enj.pdb taken from the RCSB, hydrogenated with the web client MolProbity, and renumbered for continuity as used in the publication.
Code
basic_utils.cpp
text/x-c (10kB)
Software: MIT License
Code file of basic utilities such as typical #includes and random number generation.
basic_utils.h
text/x-c (4kB)
Software: MIT License
Header file of basic utilities such as typical #includes and random number generation.
PDBobject.cpp
text/x-c (130kB)
Software: MIT License
Code file for the objects which govern the physical structure taken from the pdb file input and search for constraints as well as writing out their properties.
PDBobject.h
text/x-c (18kB)
Software: MIT License
Header file for the objects which govern the physical structure taken from the pdb file input and search for constraints as well as writing out their properties.
SBFIRST.cpp
text/x-c (2kB)
Software: MIT License
Main code file for SBFIRST constraint generation program
Vectors.cpp
text/x-c (5kB)
Software: MIT License
Code file for a cartesian xyz vector class
Vectors.h
text/x-c (1kB)
Software: MIT License
Header file for a cartesian xyz vector class
makeSB.sh
text/plain (165B)
Software: MIT License
Primitive make file for the constraint generation program
Contributors
University of Bath
Rights Holder
Documentation
Data collection method:
The .pdb files were taken from the RCSB PDB. The code files were written entirely in house unless otherwise commented and referenced within the code.
Data processing and preparation activities:
The .pdb files were hydrogenated with the web service Molprobity and renumbered by opening in a visualisation software such as Pymol or Avogadro and saving new unique atomic numbering, as Molprobity provides all new hydrogens with a serial number of 0.
Funders
University of Bath
https://doi.org/10.13039/501100000835
University of Bath studentship
ClusterVision
ClusterVision HPC scholarship
European Research Council (ERC)
https://doi.org/10.13039/501100000781
GROWMOF Modelling of MOF self-assembly, crystal growth and thin film formation
648283
Publication details
Publication date: 20 June 2019
by: University of Bath
Version: 1
DOI: https://doi.org/10.15125/BATH-00566
URL for this record: https://researchdata.bath.ac.uk/id/eprint/566
Related papers and books
McManus, T. J., Wells, S. A., and Walker, A. B., 2019. Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase. Physical Biology, 17(1), 016002. Available from: https://doi.org/10.1088/1478-3975/ab2b5c.
Contact information
Please contact the Research Data Service in the first instance for all matters concerning this item.
Contact person: Tom Mcmanus
Faculty of Engineering & Design
Chemical Engineering
Faculty of Science
Physics
