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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)
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/