5SXY | pdb_00005sxy

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5SXY | pdb_00005sxy

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)

5SXY | pdb_00005sxy