2HJJ

Solution NMR structure of protein ykfF from Escherichia coli. Northeast Structural Genomics target ER397.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_13C-separated_NOESY	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293
2	3D_15N-separated_NOESY	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293
3	3D_13C-separated_NOESY	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	100% D2O	100 mM NaCl	5.5	ambient	293
4	HNHA	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293
5	high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls)	0.95 mM 5%-13C,U-15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293
6	3D GFT backbone expts	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293
7	3D HCCH-COSY and HCCH-TOCSYs	0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5	5% D2O / 95% H2O	100 mM NaCl	5.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing	THE STRUCTURES ARE BASED ON A TOTAL OF 1044 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 72 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (17.7 CONSTRAINTS PER RESIDUE, 5.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 10 to 75 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED N- AND C- TERMINI OF THE PROTEIN WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION.	VNMR

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

Additional NMR Experimental Information

Details

THE STRUCTURE WAS DETERMINED USING GFT AND TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE FROM THE GFT DATA USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 95.3%, SIDE CHAIN, 93.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 90.9%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 10 TO 75, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 11-67,72-74: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 85.9%, ADDITIONALLY ALLOWED, 13.8%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.45/-1.46, ALL, -0.38/-2.25. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 29.98/-3.62. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.956, PRECISION, 0.934, F-MEASURE, 0.945, DP-SCORE, 0.848.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	6.1C	Varian
2	collection	TopSpin	1.3	Bruker
3	refinement	AutoAssign	2.1.1	Zimmerman, Moseley, Montelione
4	refinement	XPLOR-NIH	2.11.2	Clore et al
5	refinement	AutoStructure	2.1.1	Huang & Montelione
6	processing	AGNuS	2.0	Moseley & Montelione
7	data analysis	PdbStat	4.1	Tejero & Montelione
8	data analysis	PSVS	1.3	Bhattacharya, Hang, Montelione
9	refinement	CNS	1.1	Brunger et al