2JRO

Solution NMR Structure of SO0334 from Shewanella oneidensis. Northeast Structural Genomics Target SoR75

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
2	2D 1H-13C HSQC	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
3	3D 1H-15N NOESY	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
4	3D 1H-13C NOESY	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
5	3D 1H-13C NOESY aromatic	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
6	3D HNCO	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
7	3D HNCACB	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
8	3D NH(CO)CACB	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
9	3D HBHA(CO)NH	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
10	3D HCCH-TOCSY	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
11	3D HCCH-COSY	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
12	3D CCH-TOCSY	1.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	ambient	293
13	2D 1H-13C HSQC_high resolution	0.95 mM [U-5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3	95% H2O/5% D2O	100	6.5	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 1006 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 42 HYDROGEN BOND CONSTRAINTS (15.3 CONSTRAINTS PER RESIDUE, 4.2 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 74 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 C-TERMINAL HIS TAG RESDIUES OF THE PROTEIN (HHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED(S(PHI)+S(PSI)<1.8): 1, 6-8, 39-46, 65-74. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENT WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT (EXCLUDING C-TERMINAL HHHH): BACKBONE,98.87%, SIDE CHAIN, 94.56%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 88.23%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-74 PSVS 1.3), WHERE ORDERED RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 2-5, 9-38, 47-64.. (A) RMSD (ORDERED RESIDUES): BB 0.6, HEAVY ATOM: 1.1 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.85%, ADDITIONALLY ALLOWED: 8.5%, GENEROUSLY ALLOWED : 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.11/-0.12, ALL , -0.14/-0.83. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.48/-1.82. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, 0987, PRECISION, 0.914, F-MEASURE, 0.949, DP-SCORE, 0.788.	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)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	1.3	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	2.1.1	Huang, Tejero, Powers and Montelione
6	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7	structure solution	X-PLOR NIH	2.11.2	Schwieters, Kuszewski, Tjandra and Clore
8	refinement	X-PLOR NIH	2.11.2	Schwieters, Kuszewski, Tjandra and Clore
9	structure solution	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
10	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
11	data analysis	PSVS	1.3	Bhattacharya and Montelione
12	pdb analysis	PdbStat	4.0	Tejero and Montelione
13	structure solution	CYANA		Guntert, Mumenthaler and Wuthrich

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.