1L3N
The Solution Structure of Reduced Dimeric Copper Zinc SOD: the Structural Effects of Dimerization
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCA, 3D NH(CO)CA, 3D HNCO, 3D HN(CA)CO-TROSY like, 2D 15N-HSQC, 2D 13C-HSQC, 3D 13C-NOESY-HSQC | Cu(I),Zn(II) SOD 2mM enriched in 15N, 13C and 2H at 70% | 20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant | |||||
2 | 3D H(C)CH-TOCSY, 3D (H)CCH-TOCSY | Cu(I),Zn(II) SOD 2mM enriched in 15N, 13C | 20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant | |||||
3 | 3D 15N-NOESY-HSQC, 3D HNHA, 3D HNHB, 2D NOESY | Cu(I),Zn(II) SOD 2mM enriched in 15N | 20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant | 5.0 | 1 atm | 296 | ||
4 | 2D NOESY | Cu(I),Zn(II) SOD 2mM enriched in 15N | 20mM phosphate buffer pH5.00 10% D2O, 8mM ascorbate reductant | 5.0 | 1 atm | 286 | ||
5 | 2D 15N-HSQC | Cu(I),Zn(II) SOD 2mM enriched in 15N | 20mM phosphate buffer pH5.00 100% D2O, 8mM ascorbate reductant | 5.0 | 1 atm | 296 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 700 |
3 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing and restrained enegy minimization in vacuum | The structures were calculated using the constraints: 3566 NOE cross peaks were converted into distance constraints, 49 dihedral phi angles, 52 dihedral psi angles, 14 chi angles and 45 proton pairs stereospecifically assigned. The Cu(I) and Zn(II) metal ions were included in the calculation with special linkers. The disulfide bridge between Cys57 and Cys146 was introduced with upper and lower distance limits between the CB and SG atoms of the two side chains. | CALIBA |
NMR Ensemble Information | |
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Conformer Selection Criteria | structure with the lowest energy target function |
Conformers Calculated Total Number | 1400 |
Conformers Submitted Total Number | 30 |
Additional NMR Experimental Information | |
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Details | Cu(I), Zn(II) SOD structure was determined using triple resonance three-and bi-dimensional and homonuclear bi-dimensional techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | CALIBA | Guenter et al. | |
2 | structure solution | GLOMSA | Guenter et al. | |
3 | structure solution | DYANA | Guenter et al. | |
4 | refinement | Amber | Pearlman et al. | |
5 | collection | XwinNMR | ||
6 | data analysis | PROCHECK-NMR | Laskowski et al. |