2K49

Solution NMR structure of UPF0339 protein SO3888 from Shewanella oneidensis. Northeast Structural Genomics Consortium target SoR190

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
2	2D 1H-13C HSQC	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
3	3D 1H-15N NOESY	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
4	3D simutaneous NOESY	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
5	3D 1H-13C NOESY aromatic	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
6	3D HNCO	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
7	3D HNCACB	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
8	3D CBCA(CO)NH	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
9	3D HCCH-COSY	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
10	3D HCCH-TOCSY	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
11	3D HBHA(CO)NH	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
12	2D 1H-13C HSQC_high resolution	1.3 mM [U-5% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293
13	3D CCH-TOCSY	1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	0.1 M	5.5	ambient	293

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

NMR Refinement
Method	Details	Software
simulated annealing	THE STRUCTURES ARE BASED ON A TOTAL OF 2291 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 146 DIHEDRAL ANGLE CONSTRAINTS, AND 92 HYDROGEN BOND CONSTRAINTS (22.4 CONSTRAINTS PER RESIDUE, 7.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 118 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE AND CYANA. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS AND HAVE BEEN INCLUDED IN THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI)+S(PSI)<1.8): 1-3, 21-22, 112-118. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (TALOS) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING CYANA. COMPLETENESS OF NMR ASSIGNMENT: BACKBONE, 94.10%, SIDE CHAIN, 82.27%, AROMATICS, 76.92%, STEREOSPECIFIC METHYL, 91.67%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-118 PSVS 1.3), WHERE ORDERED RESIDUE RANGES (S(PHI)+S(PSI)>1.8) COMPRISE: 4-20, 23-111. (A) RMSD (ORDERED RESIDUES): BB 0.6, HEAVY ATOM: 1.1 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 88.1%, ADDITIONALLY ALLOWED: 11.8%, GENEROUSLY ALLOWED : 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.30/-0.87, ALL , -0.12/-0.71. (D) MOLPROBITY CLASH SCORE (RAW/Z): 13.32/-0.76. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-118): RECALL, 1, PRECISION, 0.975, F-MEASURE, 0.987, DP-SCORE, 0.89.	TopSpin

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 protein is a monomer by gel filtration chromatography and static light scattering.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	2.1	Bruker Biospin
2	chemical shift assignment	AutoAssign	2.2.1	Zimmerman, Moseley, Kulikowski and Montelione
3	peak picking	Sparky	3.110	Goddard
4	data analysis	Sparky	3.110	Goddard
5	structure solution	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
6	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
8	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
9	data analysis	PSVS	1.3	Bhattacharya and Montelione
10	pdbanalysis	PdbStat	5.0	Tejero and 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.