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REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
1.4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87); 5MM TRIS-D11; 400MM
NACL
400
6.7
AMBIENT
300
2
3D_15N-SEPARATED_NOESY
2 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11;
100MM NACL
100
6.8
AMBIENT
298
3
3D_13C-SEPARATED_NOESY
2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS-
D11; 400MM NACL
400
6.7
AMBIENT
300
4
HMQC-J
4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11;
400MM NACL
400
6.7
AMBIENT
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
GE
GN500
500
2
Varian
UNITYPLUS
600
NMR Refinement
Method
Details
Software
TORSION ANGLE DYNAMICS AND SIMULATED ANNEALING
THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE
RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS.
STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION ANGLE DYNAMICS.
THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50 STRUCTURES WITH
THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING SIMULATED
ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE SELECTED TO
REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS DISPLAYED NO NOE
VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3 DEGREES. THE
MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION OF THE
COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY POWELL ENERGY
MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS.
VNMR
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number
1
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL EXPRESSION
SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131).