Experiment: 21KO

Solution structure of fission yeast Rpb6, common subunit of RNA polymerases I, II, and III

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
2	2D 1H-15N HSQC	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 700
3	2D 1H-15N HSQC	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 950
4	3D HNCACB	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
5	3D CBCA(CO)NH	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
6	3D HNCA	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
7	3D HN(CO)CA	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
8	3D HNCO	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
9	3D HN(CA)CO	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
10	3D HBHANH	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
11	3D HBHA(CO)NH	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 600
12	3D 1H-15N NOESY	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 91 % H2O, 9 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	91% H2O/9% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 950
13	2D 1H-13C HSQC	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 100 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	100% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 950
14	2D 1H-13C HSQC aromatic	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 100 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	100% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 950
15	3D 1H-13C NOESY	1.9 mM [U-99% 13C; U-99% 15N] Rpb6, 100 % [U-2H] D2O, 20 mM potassium phosphate, 25 mM sodium chloride, 5 mM [U-2H] d-DTT	100% D2O	25mM NaCl mM	6.8	1 atm	298	Bruker AVANCE III HD 950

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	600
2	Bruker	AVANCE III HD	700
3	Bruker	AVANCE III HD	950

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH

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	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	chemical shift assignment	MAGRO		Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guentert, Kigawa and Yokoyama
3	chemical shift assignment	NMRView		Johnson, One Moon Scientific
4	data analysis	TALOS-N		Shen and Bax
5	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

21KO | pdb_000021ko

Solution structure of fission yeast Rpb6, common subunit of RNA polymerases I, II, and III