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STRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 STRUCTURES
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY (1H
6.5
303
2
13C
6.5
303
3
15N)
6.5
303
4
TOCSY
6.5
303
5
HNHA
6.5
303
6
HNHB
6.5
303
7
P.COSY
6.5
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
UP750
750
2
Bruker
AMX600
600
NMR Refinement
Method
Details
Software
molecular dynamics
PROGRAMS WRITTEN BY MICHAEL NILGES FOR SYMMETRIC DIMERS WERE USED (NILGES, M. PROTEINS 17, 297-309 (1993)). STRUCTURES WERE STARTED FROM AN EXTENDED MONOMER CONFORMATION AND RANDOM ROTATIONS WERE MADE AROUND THE PHI-PSI ANGLES. THE MONOMER WAS THEN DUPLICATED AND MOLECULAR DYNAMICS WAS PERFORMED USING NMR DISTANCE RESTRAINTS AND GENERATED SYMMETRY DISTANCE RESTRAINTS. RMSD CALCULATED BY SUPERIMPOSING STRUCTURES ON LOWEST ENERGY STRUCTURE FOR RESIDUES 33-62 OF EACH MONOMER AND 68-98 OF EACH DIMER. RMSD (ANGSTROMS): ATOMS FOR RESIDUES 33-62: 0.55 ATOMS FOR RESIDUES 33-62: 1.1 BACKBONE ATOMS FOR RESIDUES 68-98: 0.7 HEAVY ATOMS FOR RESIDUES 68-98: 1.5
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE