Dataset for "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase"

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.

Subjects:
Atomic and molecular physics
Biomolecules and biochemistry

Cite this dataset as:
Mcmanus, T., Wells, S., 2019. Dataset for "Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase". University of Bath Research Data Archive. 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

Creators

Tom Mcmanus
University of Bath

Stephen Wells
University of Bath

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 studentship

Clustervision HPC

Clustervision HPC scholarship

H2020 European Research Council (ERC)
https://doi.org/10.13039/100010663

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 articles

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. 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

Departments:

Faculty of Engineering & Design
Chemical Engineering

Faculty of Science
Physics