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Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
(1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS. (5) IPAP EXPTS FOR DIPOLAR COUPLINGS DIPOLAR COUPLINGS WERE MEASURED IN A BICELLE LIQUID CRYSTALLINE MEDIUM.
6.6
308
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX
500
2
Bruker
DMX
600
3
Bruker
DMX
750
NMR Refinement
Method
Details
Software
simulated annealing
THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT RESTRAINTS, (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J. MAGN. RESON 131, 159-162 (1998); J. MAGN 133, 216-221 (1998)), AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. PROTEIN SCI. 5, 1067-1080 (1996); J. MAGN. RESON 125, 171-177 (1997)).
IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF THE
35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE
MEAN COORDINATE POSITIONS. THE LATTER ARE OBTAINED
BY TAKING THE AVERAGE OF THE 35 SIMULATED ANNEALING
STRUCTURES BEST-FITTED TO RESIDUES 1-73 AND 101-173
OF THE PROTEIN AND RESIDUES 201-240 OF THE DNA.
RESIDUES 74-85 AND 174-185 ARE DISORDERED IN SOLUTION
AND ARE THEREFORE NOT INCLUDED IN THE COORDINATES.
THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAINED
BY RESTRAINED REGULARIZATION OF THE AVERAGE COORDINATES
AGAINST THE SAME TARGET FUNCTION USED TO CALCULATE THE
SIMULATED ANNEALING STRUCTURES.
X-PLOR/CNS
NMR Ensemble Information
Conformer Selection Criteria
REGULARIZED MEAN STRUCTURE
Conformers Calculated Total Number
35
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 SEQUENTIAL, 504 MEDIUM RANGE, 212 LONG RANGE, 616 INTRARESIDUE, 174 INTERSUBUNIT. (B) DNA: 428 INTRARESIDUE, 196 SEQUENTIAL INTRASTRAND, 24 INTERSTRAND. (C) PROTEIN- DNA 168. H-BOND RESTRAINTS: PROTEIN 138, DNA 120. TORSION ANGLE RESTRAINTS: PROTEIN 480 (142 PHI, 142 PSI, 112 CHI1, 68 CHI2, 16 CHI3), DNA 228. THREE-BOND HN-HALPHA COUPLING CONSTANTS: 72. SECONDARY 13C SHIFTS: 140 13CALPHA, 140 13CBETA. DIPOLAR COUPLINGS: 1DNH PROTEIN: 70, 1DCH DNA 70. REPULSIVE RESTRAINTS: 106