5SXY

The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE)

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCACB	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 900
2	2D 1H-15N HSQC	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 900
3	3D CBCA(CO)NH	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 900
4	3D HNCO	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
5	2D plane of 3D HCACO	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
6	3D HNHA	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
7	3D H(CCO)NH	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
8	3D C(CO)NH	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
9	3D HCCH-TOCSY	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
10	2D HBCBCGCDHD	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
11	2D HBCBCGCDCEHE	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
12	2D 1H-13C HSQC aromatic	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
13	2D 1H-13C HSQC aliphatic	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
14	2D plane of HCCH-TOCSY for aromatic ring	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 850
15	3D 15N-edited NOESY	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 900
16	3D 13C-edited NOESY	4.6 mg/mL [U-13C; U-15N] PqqD	95% H2O/5% D2O	25 mM	6.5	1 atm	298	Bruker AVANCE III 900

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	850
2	Bruker	AVANCE III	900

NMR Refinement
Method	Details	Software
simulated annealing		XPLOR-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	collection	TopSpin	3.1.6	Bruker Biospin
2	processing	NMRPipe	year 2012	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	Sparky	3	Goddard and Kneller
6	structure calculation	XPLOR-NIH	2.37	Schwieters
7	refinement	Protein Structure Validation Suite (PSVS)	1.5	http://psvs-1_5-dev.nesg.org/

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 R01GM133198.