2KOI
Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state
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 | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
2 | 3D HNCO | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
3 | 3D CBCA(CO)NH | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
4 | 3D HNCACB | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
5 | 3D C(CO)NH | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
6 | 3D H(CCO)NH | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
7 | 3D HCCH-TOCSY | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
8 | 3D 1H-15N NOESY | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
9 | 3D 1H-13C NOESY | 1.7 mM [U-13C; U-15N] SYB-CPH1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 298 | |
10 | 3D HNCO ANTIPHASE | 0.5 mM SYB-CPH1(GAF), 0.5 mM [U-13C] PHYCOCYANOBILIN, 10 mM [U-2H] TRIS-DCL, 0.03 % sodium azide | 93% H2O/7% D2O | 10 | 8.5 | ambient | 306 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
2 | Varian | INOVA | 600 |
3 | Bruker | DMX | 600 |
4 | Bruker | DMX | 750 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle molecular dynamics, internal variable dynamics | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | peak picking | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | chemical shift assignment | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
6 | data analysis | PIPP | Garrett | |
7 | peak picking | PIPP | Garrett | |
8 | chemical shift assignment | PIPP | Garrett | |
9 | geometry optimization | X-PLOR_NIH | Schwieters, Kuszewski, Tjandra and Clore | |
10 | structure solution | X-PLOR_NIH | Schwieters, Kuszewski, Tjandra and Clore | |
11 | refinement | X-PLOR_NIH | Schwieters, Kuszewski, Tjandra and Clore | |
12 | collection | VNMRJ | Varian | |
13 | data analysis | Molmol | Koradi, Billeter and Wuthrich | |
14 | data analysis | ProcheckNMR | Laskowski and MacArthur |