2L0D
Solution NMR Structure of putative cell surface protein MA_4588 (272-376 domain) from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR254A
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
2 | 2D 1H-13C HSQC | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
3 | 3D HNCO | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
4 | 3D CBCA(CO)NH | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
5 | 3D HNCACB | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
6 | 3D 1H-13C arom NOESY | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
7 | 3D 1H-13C aliph NOESY | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
8 | 3D 1H-15N NOESY | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
9 | 4D 1H-13C-13C-1H HMQC-NOESY-HMQC | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 100% D2O | 6.5 | ambient | 298 | ||
10 | 3D HBHA(CO)NH | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
11 | 3D HCCH-TOCSY | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
12 | 3D C(CO)NH | 1.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
13 | 2D 1H-13C HSQC | 1.1 mM [5% biosynthetically-directed 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3 | 95% H2O/5% D2O | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 750 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics and simulated annealing | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 40 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
2 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
3 | geometry optimization | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
4 | refinement | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
5 | geometry optimization | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
6 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
7 | data analysis | AutoStructure | 2.1 | Huang, Tejero, Powers and Montelione |
8 | data analysis | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
9 | chemical shift assignment | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
10 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
11 | data analysis | XEASY | Bartels et al. | |
12 | peak picking | XEASY | Bartels et al. | |
13 | chemical shift assignment | XEASY | Bartels et al. | |
14 | collection | TopSpin | Bruker Biospin | |
15 | collection | VnmrJ | Varian | |
16 | chemical shift assignment | PINE | Bahrami, Markley, Assadi, and Eghbalnia | |
17 | data analysis | Sparky | Goddard | |
18 | geometry optimization | TALOS+ | Shen, Cornilescu, Delaglio and Bax | |
19 | geometry optimization | PALES | PALES (Zweckstetter, Bax) | |
20 | geometry optimization | REDCAT | Valafar, Prestegard | |
21 | refinement | AutoStructure | 2.1 | Huang, Tejero, Powers and Montelione |
22 | refinement | Xplor-NIH | Schwieters, Kuszewski, Tjandra and Clore |