2O8K

NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D_C13-seperated[F1], C12-filtered[F2] NOESY1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O250 mM NaCl6.9ambient303
23D_C13-seperated_NOESY1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O250 mM NaCl6.9ambient303
33D_15N-seperated_NOESY1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O250 mM NaCl6.9ambient303
42D_C12-filtered[F1,F2] NOESY1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O250 mM NaCl6.9ambient303
52D_C12-filtered[F1] NOESY1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O250 mM NaCl6.9ambient303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDMX600
2BrukerAVANCE600
3BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
docking, rigid-body minimization, simulated annealingprotein and DNA structures determined individually via simulated annealing; the two structures were docked using rigid body minimization; the whole structure was refined by simulated annealingNMRPipe
NMR Ensemble Information
Conformer Selection Criteria20 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively
Conformers Calculated Total Number50
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipe2.3Delaglio et al. 1995
2data analysisNMRView5.0.4Johnson et al. 1994
3structure solutionCYANA2.1Guntert 2004
4refinementX-PLOR2.14Schwieters et al. 2003