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Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
3D_15N-separated_NOESY
2mM LAC-HP62-V52C U-15N,13C, 60mM KPI, 400mM KCL
90% H2O/10% D2O
400mM KCl, 60mM KPi
5.8
ambient
300
2
3D_13C-separated_NOESY
2mM LAC-HP62-V52C U-15N,13C, 60mM KPI, 400mM KCL
90% H2O/10% D2O
400mM KCl, 60mM KPi
5.8
ambient
300
3
13C-15N double-half noesy filter
2mM LAC-HP62-V52C U-15N,13C, 60mM KPI, 400mM KCL
90% H2O/10% D2O
400mM KCl, 60mM KPi
5.8
ambient
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
750
NMR Refinement
Method
Details
Software
THE STRUCTURE OF THE COMPLEX WAS CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LACHP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE 100 BEST STRUCTURES WERE SELECTED AND DOCKED ONTO THE NONSPECIFIC LAC OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE AND PLANARITY RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA CLOSE TO B-DNA CONFORMATION.
THE STRUCTURE OF THE COMPLEX WAS SOLVED ON THE BASIS OF 70 INTERMOLECULAR RESTRAINTS
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
400
Conformers Submitted Total Number
20
Representative Model
1 (closest to the average)
Additional NMR Experimental Information
Details
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMO- AND HETERONUCLEAR TECHNIQUES. 13C-15N LABELED PROTEIN AND UNLABELED NUCLEOTIDE WERE USED. IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES.