1L6N | pdb_00001l6n

STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG POLYPROTEIN

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	4D_13C-separated_NOESY	1mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME	95% H2O/5% D2O
2	4D_13C/15N-separated_NOESY	1mM U-15N,13C gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME	95% H2O/5% D2O	50	5.0	1 atm	303
3	3D_15N-separated_NOESY	1mM U-15N gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME	95% H2O/5% D2O	50	5.0	1 atm	303
4	4D_15N/15N-separated_NOESY	1mM U-15N,2H gag283, 50mM acetate buffer(pH5.0), 100mM NaCl, 5mM BME	95% H2O/5% D2O	50	5.0	1 atm	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DMX	600

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics	20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR MATRIX AND CAPSID N-TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. UNAMBIGUOUS H-BONDS WERE ALSO INCORPORATED TO REINFORCE CANONICAL SECONDARY STRUCTURE. THE INITIAL STRUCTURES WERE THEN USED TO ASSESS THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. FINALLY, ALL THE CONSTRAINTS WERE USED TO CALCULATE THE STRUCTURE OF THE WHOLE PROTEIN.	DYANA

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	DYANA	1.5	Guentert
2	processing	NMRPipe	2.0	Delaglio
3	collection	XwinNMR	2.6
4	refinement	DYANA	1.5	Guentert,P., Mumenthaler,C., & Wuthrich,K.