2G7J

Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	5% D2O/95% H2O	100 mM NaCl	6.5	ambient	293
2	3D_13C-separated_NOESY	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	100% D2O	100 mM NaCl	6.5	ambient	293
3	4D_13C-separated_NOESY	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	100% D2O	100 mM NaCl	6.5	ambient	293
4	HNHA	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	5% D2O/95% H2O	100 mM NaCl	6.5	ambient	293
5	high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls)	1.07mM 5%-13C,U-15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	5% D2O/95% H2O	100 mM NaCl	6.5	ambient	293
6	backbone TR expts	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	5% D2O/95% H2O	100 mM NaCl	6.5	ambient	293
7	3D HCCH-COSY	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	100% D2O	100 mM NaCl	6.5	ambient	293
8	3D TOCSYs, aromatic expts	1.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5	5% D2O/95% H2O	100 mM NaCl	6.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Avance	600
2	Varian	INOVA	600
3	Varian	INOVA	750

NMR Refinement
Method	Details	Software
simulated annealing	THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS PER RESIDUE, 6.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 to 112 BY PSVS 1.2). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED C-TERMINUS OF THE PROTEIN (EKTD + LEHHHHHH TAG) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION.	XWINNMR

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 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE 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 HYPER AND TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 to 112, PSVS 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3-43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, 0.846.

Additional NMR Experimental Information

Details

THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE 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 HYPER AND TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 to 112, PSVS 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3-43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, 0.846.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XWINNMR	3.5pl6	Bruker
2	collection	VNMR	6.1C	Varian
3	data analysis	Sparky	3.110	Goddard & Kneller
4	data analysis	AUTOASSIGN	1.17.0	Zimmerman, Moseley, Montelione
5	refinement	AUTOSTRUCTURE	2.1.1	Huang & Montelione
6	refinement	XPLOR-NIH	2.11.2	Clore et al.
7	refinement	CNS	1.1	Brunger et al.
8	data analysis	PDBstat	4.01	Tejero & Montelione
9	data analysis	PSVS	1.2	Bhattacharya & Montelione

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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2G7J

Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72.