2K5W

Solution NMR Structure of Putative Lipoprotein from Bacillus cereus Ordered Locus BC_2438. Northeast Structural Genomics Target BcR103A.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
2	2D 1H-13C HSQC	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
3	3D 1H-13C NOESY ARO	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
4	3D 1H-13C-15N SIM NOESY	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
5	3D HNCO	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
6	3D HNCACB	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
7	3D HBHA(CO)NH	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
8	3D CBCA(CO)NH	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
9	3D HNCA	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
10	3D HN(CO)CA	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
11	3D HCCH-TOCSY	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
12	3D HCCH-COSY	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
13	3D CCH-TOCSY	0.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
14	2D 1H-15N HSQC	1.37 mM [5% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
15	2D 1H-13C HSQC stereo	1.37 mM [5% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
16	HETNOE	1.37 mM [5% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	90% H2O/10% D2O	0.1	6.5	ambient	298
17	slow exch 1H-15N HSQC	0.5 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	100% D2O	0.1	6.5	ambient	298
18	3D 1H-13C NOESY	0.5 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride	100% D2O	0.1	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	AVANCE	600
3	Varian	INOVA	500

NMR Refinement
Method	Details	Software
torsion angle dynamics	MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 85.1%, SIDECHAIN 78.2%, AROMATIC (SC) 76.7%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1446 NOE, 137 DIHE. MAX NOE VIOLATION: 0.36 A (1MODEL); MAX DIHE VIOLATION: 6.6 DEG. 16 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 9-11, 13-18,23-51, 67-75, 87-107 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (13-17, 24-27, 30-33, 35-41, 46-51, 67-72, 87-93). RMSD 1.0 BACKBONE, 1.3 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 95.7/4.2/0.1/0.0. PROCHECK (PSI-PHI): -0.31/-0.90(RAW/Z), PROCHECK (ALL): -0.16/-0.95 (RAW/Z), MOLPROBITY CLASH: 15.17/-1.08 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.99, PRECISION: 0.90, F-MEASURE: 0.94 DP-SCORE: 0.803.	CYANA

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	chemical shift assignment	AutoAssign	2.4.0	Zimmerman, Moseley, Kulikowski and Montelione
3	collection	TopSpin	2.1	Bruker Biospin
4	refinement	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
5	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
7	data analysis	Sparky	3.113	Goddard
8	validation	PSVS	1.3	Bhattacharya and Montelione
9	validation	PdbStat	5.1	Tejero R.; Montelione GT
10	visualization	MOLMOL	2k2	Koradi, Billeter and Wuthrich
11	validation	Procheck		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho
12	validation	MolProbity		Richardson

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.