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NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
1H-15N HSQC
95% D2O / 5% WATER
100 mM
5.8
1.0 atm
303.0
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
750
NMR Refinement
Method
Details
Software
HADDOCK
STRUCTURE OF THE COMPLEX WAS CALCULATED WITH HADDOCK FOLLOWING STANDARD PROTOCOLS DOMINGUEZ, BOELENS AND BONVIN, JACS 2003, 125, 1731-1737
CNS
NMR Ensemble Information
Conformer Selection Criteria
LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER
Conformers Calculated Total Number
200
Conformers Submitted Total Number
10
Representative Model
1 (n/a)
Additional NMR Experimental Information
Details
THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 28 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA, MUTAGENESIS DATA AND KNOWN RNA CLEAVAGE MECHANISM, USING THE CRYSTAL STRUCTURE OF THE KID DIMER (PDB ENTRY 1M1F) AS STARTING POINT. THE CHEMICAL SHIFT PERTURBATION DATA WERE OBTAINED BY ANALYSIS OF 1H-15N HSQC SPECTRA RECORDED WITH INCREASING RNA CONCENTRATIONS.