2LR3
Solution structure of the anti-fungal defensin DEF4 (MTR_8g070770) from Medicago truncatula (barrel clover)
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 mM [U-99% 15N] protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 | |
2 | 2D 1H-13C HSQC | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 100% D2O | 0.01 | 4.4 | ambient | 293 | |
3 | 2D 1H-1H TOCSY | 1 mM protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 | |
4 | 2D 1H-1H TOCSY | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 100% D2O | 0.01 | 4.4 | ambient | 293 | |
5 | 2D 1H-1H NOESY | 1 mM protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 | |
6 | 2D 1H-1H NOESY | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 100% D2O | 0.01 | 4.4 | ambient | 293 | |
7 | 3D 1H-15N NOESY | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 | |
8 | 3D 1H-15N TOCSY | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 | |
9 | deuterium exchange | 1 mM [U-99% 15N] protein, 0.01 mM TRIS | 93% H2O/7% D2O | 0.01 | 4.4 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | VNMRS | 750 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics | STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. Oxidation of all the cys residues was confirmed by the C-beta chemical shifts for the CYS residues determined from a natural abundance 1H-13C-HSQC spectrum. Restraints for the disfulfide bonds were introduced on the basis of position in similar sequences. | Sparky |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Sparky | 3.115 | Goddard |
2 | peak picking | Sparky | 3.115 | Goddard |
3 | processing | Felix | 2007 | Accelrys Software Inc. |
4 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
5 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
6 | data analysis | PSVS | 1.3 | Bhattacharya and Montelione |
7 | refinement | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |