Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Expression of 6-His Tagged MppA
2.2. Purification of MppA
2.3. Crystallization of MppA and X-Ray Data Collection
2.4. Structure Solution by Molecular Replacement
2.5. Structure Refinement
3. Results
3.1. Expression, Purification, Crystallization, and Structure Solution of MppA
3.2. Overall Structure of MppA
3.3. Tris Binding Site
4. Discussion
Comparison to the Ligand-Bound Conformation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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A. Data statistics | ||
Resolution | 50–1.5 Å | |
Space group | P21 | |
Unit cell dimensions | a = 74.97, b = 76.81, c = 89.57, β = 91.58 | |
Number of unique reflections | 161,107 | |
Completeness | 99.6% | |
I/σ(I) | 6.82 | |
B. Refinement | ||
Resolution range (refinement) | 35–1.5 Å | |
Crystallographic R-factor a (Rwork) | 0.18 | |
Free R-factor b (Rfree) | 0.205 | |
Number per asymmetric unit | ||
MppA molecules | 2 | |
Tris molecules | 1 | |
Protein atoms | 8150 | |
Solvent atoms | 1647 | |
Deviation from standard geometry (Gfactors c) | ||
Dihedral angles | ||
Phi-psi distribution | −0.10 | |
Chi1-chi2 distribution | 0.12 | |
Chi1 only | 0.19 | |
Chi3 and Chi4 | 0.59 | |
Omega | 0.54 | |
Main-chain covalent forces | ||
Main-chain bond lengths | 0.68 | |
Main-chain bond angles | 0.45 | |
Average B value (Å2) | ||
All atoms | 16.1 | |
of protein | 13.7 | |
of Tris ligand | 26.1 | |
of waters | 28.0 | |
Ramachandran plot statistics from ProCheck | ||
Number of residues Percent | ||
Most favored regions | 817 | 90.5 |
Additional allowed regions | 84 | 9.3 |
Generously allowed regions | 1 | 0.1 |
Disallowed regions | 1 | 0.1 |
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Bhatt, F.; Patel, V.; Jeffery, C.J. Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. Biology 2018, 7, 30. https://doi.org/10.3390/biology7020030
Bhatt F, Patel V, Jeffery CJ. Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. Biology. 2018; 7(2):30. https://doi.org/10.3390/biology7020030
Chicago/Turabian StyleBhatt, Forum, Vishal Patel, and Constance J. Jeffery. 2018. "Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution" Biology 7, no. 2: 30. https://doi.org/10.3390/biology7020030
APA StyleBhatt, F., Patel, V., & Jeffery, C. J. (2018). Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. Biology, 7(2), 30. https://doi.org/10.3390/biology7020030