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Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state
NMR Experiment 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 Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 800 2 Varian INOVA 600 3 Bruker DMX 600 4 Bruker DMX 750
NMR Refinement Method Details Software torsion angle molecular dynamics, internal variable dynamics NMRPipe
NMR Ensemble Information 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 # 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