1DK3

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).

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	4.3	VARIAN
2	processing	Felix	95	HARE, BIOSYM
3	data analysis	XEASY	1.3.13	BARTLES
4	structure solution	DYANA	1.5	GUENTERT
5	refinement	X-PLOR	4.0	BRUNGER

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.