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 | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 850 |
2 | Bruker | AVANCE III | 900 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | XPLOR-NIH |
NMR Ensemble Information | |
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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 | ||||
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# | 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/ |