7BQD

Solution NMR structure of NF8 (knot fold); de novo designed protein with a novel fold


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
22D 1H-13C HSQC aliphatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
32D 1H-13C HSQC aromatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
43D BEST-HNCO0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
53D BEST-HNCACB0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
63D BEST-HN(CO)CACB0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
73D HCCH-TOCSY aliphatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
83D HCCH-TOCSY aromatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
93D 1H-15N NOESY0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
103D 1H-13C NOESY aliphatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
113D 1H-13C NOESY aromatic0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
122D 1H-15N HSQC IPAP0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
132D 1H-15N HSQC IPAP0.2 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride, 10 mg/mL Pf1 phage95% H2O/5% D2O56.5 mM6.81 atm303Bruker AVANCE III 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III800
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriatarget function
Conformers Calculated Total Number200
Conformers Submitted Total Number20
Representative Model1 (target function)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpin3.2Bruker Biospin
2peak pickingMAGRO2.01.38Updated version of Kujira (Kobayashi, N. et al., 2007)
3processingNMRPipe2017Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4data analysisNMRView9.0Johnson, One Moon Scientific
5chemical shift assignmentCYANA3.98Guntert, Mumenthaler and Wuthrich
6data analysisTALOS2017Cornilescu, Delaglio and Bax
7structure calculationCYANA3.98Guntert, Mumenthaler and Wuthrich
8refinementAmber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman