2HJQ

NMR Structure of Bacillus Subtilis Protein YqbF, Northeast Structural Genomics Target SR449

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_13C-separated_NOESY	1.3mM YqbF, U-N15, 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O	95% H2O/5% D2O	100 mM NaCl	5.5	ambient	298
2	3D_15N-separated_NOESY	0.7mM YqbF, U-N15, 5% 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O	95% H2O/5% D2O	100 mM NaCl	5.5	ambient	298
3	4D_13C-separated_NOESY	1.3mM YqbF, U-N15, 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3	100% D2O	100 mM NaCl	5.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	800
3	Varian	INOVA	900

NMR Refinement
Method	Details	Software
distance geometry simulated annealing, CNS water refinement		Sparky

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest bond energy
Conformers Calculated Total Number	30
Conformers Submitted Total Number	20
Representative Model	1 (lowest total energy)

Additional NMR Experimental Information
Details	THE STRUCTURES ARE BASED ON A TOTAL OF 1719 RESTRAINTS. 1536 are NOE-DERIVED; INTRA-RESIDUE [i=j] = 268; SEQUENTIAL [(I-J)=1] = 437 MEDIUM RANGE [1<(I-J)<5] = 387; LONG RANGE [(I-J)>=5] = 444; HYDROGEN BOND RESTRAINTS = 42 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 16.3 (RESIDES 2-47,57-104); DIHEDRAL-ANGLE RESTRAINTS = 141 (70 PHI, 71 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 18.3 (RESIDES 2-47,57-104); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 4.7 NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.06 ANGSTROMS.; MAXIMUM DISTANCE VIOLATION 0.05 ANG. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >10 DEG = 0 MAX DIHEDRAL ANGLE VIOLATION = 0.5 DEG. AVERAGE RMS ANGLE VIOLATION / CONSTRAINT = 0.003 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.5 ANG; ALL HEAVY ATOMS = 0.9 ANG (RESIDUES 2-47) RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.7 ANG; ALL HEAVY ATOMS = 1.3 ANG (RESIDUES 57-98) PROCHECK (RESIDUES 2-47,57-104): MOST FAVORED REGIONS = 89% ADDITIONAL ALLOWED REGIONS = 10%; GENEROUSLY ALLOWED REGIONS = 0%; DISALLOWED REGIONS = 1%. 6 NON-NATIVE N-TERMINAL RESIDUES (MAGDPL) AND 8 C-TERMINAL RESDIUES, INLUDING THE HIS TAG, (LEHHHHHH) WERE INCLUDED IN THE STRUCTURE CALCULATION.

Additional NMR Experimental Information

Details

THE STRUCTURES ARE BASED ON A TOTAL OF 1719 RESTRAINTS. 1536 are NOE-DERIVED; INTRA-RESIDUE [i=j] = 268; SEQUENTIAL [(I-J)=1] = 437 MEDIUM RANGE [1<(I-J)<5] = 387; LONG RANGE [(I-J)>=5] = 444; HYDROGEN BOND RESTRAINTS = 42 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 16.3 (RESIDES 2-47,57-104); DIHEDRAL-ANGLE RESTRAINTS = 141 (70 PHI, 71 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 18.3 (RESIDES 2-47,57-104); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 4.7 NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.06 ANGSTROMS.; MAXIMUM DISTANCE VIOLATION 0.05 ANG. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >10 DEG = 0 MAX DIHEDRAL ANGLE VIOLATION = 0.5 DEG. AVERAGE RMS ANGLE VIOLATION / CONSTRAINT = 0.003 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.5 ANG; ALL HEAVY ATOMS = 0.9 ANG (RESIDUES 2-47) RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.7 ANG; ALL HEAVY ATOMS = 1.3 ANG (RESIDUES 57-98) PROCHECK (RESIDUES 2-47,57-104): MOST FAVORED REGIONS = 89% ADDITIONAL ALLOWED REGIONS = 10%; GENEROUSLY ALLOWED REGIONS = 0%; DISALLOWED REGIONS = 1%. 6 NON-NATIVE N-TERMINAL RESIDUES (MAGDPL) AND 8 C-TERMINAL RESDIUES, INLUDING THE HIS TAG, (LEHHHHHH) WERE INCLUDED IN THE STRUCTURE CALCULATION.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Sparky	3.1	T.D. Goddard, D.G. Kneller
2	processing	NMRPipe	Linuz9	F. Delaglio, A. Bax
3	refinement	xplor-NIH	2.15.0	C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore
4	refinement	CNS	1.1	A. Brunger, G. L .Warren
5	collection	VNMR	6.1c	Varian

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.

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2HJQ

NMR Structure of Bacillus Subtilis Protein YqbF, Northeast Structural Genomics Target SR449