Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA
SOLUTION NMR - THEORETICAL MODEL
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY
100 MM NACL, 5 MM MGCL2
6.2
1 atm
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
600
NMR Refinement
Method
Details
Software
DOCKING/MODELING
THE COORDINATES OF THE PROTEIN, RNA AND THE ANTIBIOTIC WERE HELD RIGID DURING REFINEMENT. THE COORDINATES OF THE RIBOSOMAL L11 (CHAIN A) AND THE RNA (CHAIN C) WERE FROM PDB ENTRY 1MMS. THE COORDINATES OF THE ANTIBIOTIC THIOSTREPTON (CHAIN B) WERE FROM PDB ENTRY 1E9W. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION.
rDOCK
NMR Ensemble Information
Conformer Selection Criteria
LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE
Conformers Calculated Total Number
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
BEST OVERALL DOCKING SCORE AND LEAST RESTRAINT VIOLATION. THE NOES INCLUDED IN THE RESTRAINTED MODELING WERE OBTAINED FROM A FILTERED NOESY EXPERIMENT ON A COMPLEX OF UNLABELED THIOSTREPTON WITH THE RNA. AS ALL INTERNAL COORDINATES WERE HELD RIGID ACCORDING TO THE X-RAY STRUCTURES, ONLY INTERMOLECULAR NOES WERE INCLUDED. ASSIGNMENTS FOR RNA WERE CHOSEN FROM AN ITERATIVE DOCKING PROCESS (SEE LENTZEN ET AL AND MANUSCRIPT TO BE PUBLISHED)
