6QBJ
Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O | 50% H2O/50% D2O | 0.05 mM | 5 | 1 atm | 303 | Agilent Uniform NMR System 800 |
2 | 2D 1H-1H NOESY | 2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O | 50% H2O/50% D2O | 0.05 mM | 5 | 1 atm | 303 | Agilent Uniform NMR System 800 |
3 | 2D DQF-COSY | 2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O | 50% H2O/50% D2O | 0.05 mM | 5 | 1 atm | 303 | Agilent Uniform NMR System 800 |
4 | 2D 1H-1H ROESY | 2.7 mM TMC.BHV, 100 mM DPC, 0.01 mM acetic acid -d4, 90 % H2O, 10 % D2O | 50% H2O/50% D2O | 0.05 mM | 5 | 1 atm | 303 | Agilent Uniform NMR System 800 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Agilent | Uniform NMR System | 800 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard |