1D9S | pdb_00001d9s

TUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-SEPARATED_NOESY	0.2 MM P15, U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA	95% H2O/5% D2O	0.1	7.5	AMBIENT	293
2	HNCA	0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA	95% H2O/5% D2O	0.1	7.5	AMBIENT	293
3	CBCA(CO)NH	0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA	95% H2O/5% D2O	0.1	7.5	AMBIENT	293
4	3D_13C-SEPARATED_NOESY	0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA	100% D2O	0.1	7.5	AMBIENT	293
5	3D_13C-SEPARATED_TOCSY	0.2 MM P15, U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA	100% D2O	0.1	7.5	AMBIENT	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	800
2	Bruker	DMX	600

NMR Refinement
Method	Details	Software
COMPARATIVE MODELING, RESTRAINT ENERGY MINIMIZATION	DUE TO THE STRUCTURAL FLEXIBILITY AND INSTABILITY OF P15, ONLY A LIMITED NUMBER OF NMR CONSTRAINTS WERE COLLECTED. BECAUSE P15 SHARES MORE THAN 85% SEQUENCE HOMOLOGY WITH P16, 19 P15 STRUCTURES WERE GENERATED BY USING COMPARATIVE MODELING (MODELLER-4) WITH AN ENSEMBLE OF P16(INK4A) NMR STRUCTURES AS TEMPLATES. THE MODELING STRUCTURES WERE THEN SUBJECTED TO 1400 STEPS OF RESTRAINT ENERGY MINIMIZATION (X-PLOR) WITH THE NMR DATA (672 DISTANCE CONSTRAINTS). THE STRUCTURES THAT SATISFY THE NMR CONSTRAINTS WERE PICKED TO REPRESENT P15(INK4B).	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers Calculated Total Number	19
Conformers Submitted Total Number	10
Representative Model	10 (minimized average structure)

Additional NMR Experimental Information
Details	TRIPLE-RESONANCE NMR SPECTROSCOPY WAS USED TO DETERMINE THE P15 STRUCTURE

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.1	BRUKER
2	refinement	X-PLOR	3.1	BRUNGER
3	structure solution	MODELLER-4	4.0	SALI