2KOI | pdb_00002koi

Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state

SOLUTION NMR

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.