8UBH
Solution NMR structure of KaiB variant from Thermosynechococcus elongatus vestitus (KaiBTV-4)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HSQC aliphatic | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 750 |
2 | 2D 1H-13C HSQC aromatic | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
3 | 3D CBCA(CO)NH | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 750 |
4 | 3D HNCA | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 750 |
5 | 3D HNCACB | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 750 |
6 | 2D 1H-15N HSQC | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 750 |
10 | 3D 1H-13C NOESY aliphatic | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
9 | 3D 1H-13C NOESY aromatic | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
8 | 3D C(CO)NH | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 600 |
7 | 3D HBHA(CO)NH | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
11 | 3D H(CCO)NH | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Bruker AVANCE III HD 600 |
12 | 3D HCCH-TOCSY | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
13 | 3D 1H-15N NOESY | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
14 | 2D (HB)CB(CGCDCE)HDH AROMATIC | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
15 | 2D (HB)CB(CGCD)HD AROMATIC | 100 mM MOPS, 50 mM sodium chloride, 2 mM TCEP | 90% H2O/10% D2O | 50 mM | 6.5 | 1 atm | 308 | Varian Uniform NMR System 800 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III HD | 750 |
2 | Bruker | AVANCE NEO | 800 |
3 | Bruker | AVANCE III HD | 600 |
4 | Varian | Uniform NMR System | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | Poky | Manthey, I. et al. POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data. J Struct Biol X 6, 100073 (2022). https://doi.org:10.1016/j.yjsbx.2022.100073 | |
5 | chemical shift assignment | PINE Server | Lee, W. et al. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73, 213-222 (2019). https://doi.org:10.1007/s10858-019-00255-3 | |
6 | collection | TopSpin | Bruker Biospin | |
7 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | structure calculation | PONDEROSA-C/S | Lee, W., Stark, J. L. & Markley, J. L. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR 60, 73-75 (2014). https://doi.org:10.1007/s10858-014-9855-x | |
8 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
10 | structure calculation | AUDANA | Lee, W., Petit, C. M., Cornilescu, G., Stark, J. L. & Markley, J. L. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR 65, 51-57 (2016). https://doi.org:10.1007/s10858-016-0036-y | |
11 | structure calculation | TALOS-N | Shen, Y. & Bax, A. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol Biol 1260, 17-32 (2015). https://doi.org:10.1007/978-1-4939-2239-0_2 |