The Crystal Structure of Bacillus cereus HblL1
Abstract
:1. Introduction
2. Results and Discussion
2.1. Structure Description
2.2. Comparison with Related Structures
2.3. Modelling HblL1-HblB Interactions
2.4. The Alpha Helical Pore Forming Toxins
3. Conclusions
4. Materials and Methods
4.1. Protein Purification
4.2. Crystallisation and Structure Determination
4.3. Molecular Docking
4.3.1. Docking
4.3.2. Interface Analysis
4.3.3. Molecular Dynamics
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
References
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PDB Entry | HblL1 |
---|---|
Data Collection | |
Accession Code | 7NMQ |
Wavelength | 0.91587 |
Crystallisation Condition | 0.1 M cacodylate Bis Tris propionate, 25% w/v PEG 1500, pH 4.0 |
Crystal Data | |
a, b, c (Å) | 36.66, 72.96, 133.05 |
α, β, γ | 90.0, 90.0, 90.0 |
Space group | P 21 21 21 |
Resolution (Å) | 1.36–63.97 |
Outer shell | 1.36–1.38 |
R-merge (%) | 6.3 (135.7) |
R-pim | 3.9 (95.2) |
R-meas (%) | 7.0 (153.4) |
CC1/2 | 0.999 (0.397) |
I/σ(I) | 12.5 (1.0) |
Completeness (%) | 99.3 (99.0) |
Multiplicity | 5.5 (4.6) |
Total Measurements | 423,755 (16,876) |
Unique Reflections | 77,106 (3698) |
Wilson B-factor(Å2) | 12.7 |
Refinement Statistics | |
Non-H Atoms | 3498 |
R-work reflections | 73,264 |
R-free reflections | 3764 |
R-work/R-free | 16.2/19.9 |
Rms Deviations | |
Bond lengths (Å) | 0.013 |
Bond Angles (°) | 1.686 |
1 Coordinate error | 0.048 |
Mean B value (Å2) | 17.4 |
Ramachandran Statistics | |
Favoured/allowed/Outliers | 290/7/0 |
% | 97.4/2.6/0.0 |
RosettaDock | PDBePISA | |||||
---|---|---|---|---|---|---|
Model | Total Energy (REU) | Interface Score (REU) | Interface Area (Å2) | ΔiG (kcal mol−1) | H Bonds | Salt Bridges |
r1 | −1235.6 | −30.3 | 1042.3 | −2.3 | 6 | 4 |
r2 | −1235.5 | −32.8 | 1000.9 | −3.9 | 7 | 2 |
r3 | −1234.9 | −30.0 | 968.1 | −3.2 | 4 | 2 |
r4 | −1234.8 | −32.1 | 1016.2 | −3.0 | 7 | 3 |
r5 | −1234.7 | −30.9 | 1025.9 | −3.8 | 6 | 4 |
r6 | −1234.6 | −31.0 | 1034.9 | −3.7 | 6 | 4 |
r7 | −1234.3 | −30.6 | 1021.6 | −3.0 | 6 | 5 |
r8 | −1234.3 | −29.3 | 1004.6 | −5.8 | 4 | 3 |
r9 | −1234.0 | −30.4 | 966.0 | −1.1 | 8 | 2 |
r10 | −1233.8 | −30.2 | 991.3 | −3.9 | 7 | 4 |
HblL1 | HblB | Type of Interaction |
---|---|---|
Ile259 | Asp12 | Hydrogen bond |
Ala276 | Thr278 | Hydrogen bond |
Gly281 | Arg150 | Hydrogen bond |
Lys381 | Glu186 | Hydrogen bond, salt bridge |
Lys392 | Asp268 | Hydrogen bond, salt bridge |
Lys404 | Gln286 | Hydrogen bond |
Lys404 | Asp12 | Hydrogen bond |
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Worthy, H.L.; Williamson, L.J.; Auhim, H.S.; Leppla, S.H.; Sastalla, I.; Jones, D.D.; Rizkallah, P.J.; Berry, C. The Crystal Structure of Bacillus cereus HblL1. Toxins 2021, 13, 253. https://doi.org/10.3390/toxins13040253
Worthy HL, Williamson LJ, Auhim HS, Leppla SH, Sastalla I, Jones DD, Rizkallah PJ, Berry C. The Crystal Structure of Bacillus cereus HblL1. Toxins. 2021; 13(4):253. https://doi.org/10.3390/toxins13040253
Chicago/Turabian StyleWorthy, Harley L., Lainey J. Williamson, Husam Sabah Auhim, Stephen H. Leppla, Inka Sastalla, D. Dafydd Jones, Pierre J. Rizkallah, and Colin Berry. 2021. "The Crystal Structure of Bacillus cereus HblL1" Toxins 13, no. 4: 253. https://doi.org/10.3390/toxins13040253