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 2JQ7 | pdb_00002jq7

Model for thiostrepton binding to the ribosomal L11-RNA


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
1IPAP(1H, 15N)HSQC0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE95% H2O/5% D2O2206.11 atm298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE DRX600
NMR Refinement
MethodDetailsSoftware
DOCKINGFOR CHAIN A, THE INITIAL COORDINATES ARE OPTIMIZED USING RDCS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN C, THE INITIAL COORDINATES ARE FROM PDB ENTRY 1E9W. LEFT FLEXIBLE ACIDS AND NUCLEIC ACIDS WHICH DO NOT COMPLY WELL WITH THE ANTIBIOTIC IN THE CASE HERE.HADDOCK
NMR Ensemble Information
Conformer Selection CriteriaTOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA
Conformers Calculated Total Number200
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsTHE RDC DATA WAS USED TO DETERMINE THE RELATIVE DOMAIN ORIENTATION OF THE L11 PROTEIN
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementHADDOCK2.0_DEVELDOMINGUEZ ET AL.
2collectionTopSpin1.3Bruker Biospin
3collectionXwinNMR3.5Bruker Biospin
4processingNMRPipe2.5Delaglio et al.
5data analysisSparky3.112Goddard et al.
6structure solutionCNS1.1Brunger et al.