2LJY
Haddock model structure of the N-terminal domain dimer of HPV16 E6
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 | 0.3 mM [U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
2 | 2D 1H-13C HSQC aliphatic | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
3 | 2D 1H-13C HSQC aromatic | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
4 | 3D HNCA | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
5 | 3D HNCACB | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
6 | 3D HN(CO)CA | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
7 | 3D HCCH-TOCSY | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
8 | 3D HCCH-COSY | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
9 | 3D 1H-15N NOESY | 0.3 mM [U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
10 | 3D 1H-13C NOESY aliphatic | 0.3 mM [U-100% 13C; U-100% 15N] E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
11 | 2D 1H-1H NOESY | 0.3 mM E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 | |
12 | 2D 1H-1H NOESY | 0.3 mM E6 | 90% H2O/10% D2O | 50 mM NaCl | 6.8 | ambient | 296 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | TopSpin |
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) |
Additional NMR Experimental Information | |
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Details | The dimer structures were calculated using Ambiguous Interaction restrains, unambiguous inter-molecular NOE-derived distance restraints and dihedral angles. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 2.1 | Bruker Biospin |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | CARA | 1.8.3 | Keller and Wuthrich |
4 | structure calculation | HADDOCK_webserver | Utrecht Biomolecular Interaction web portal | |
5 | refinement | HADDOCK_webserver | Utrecht Biomolecular Interaction web portal |