2JXP | pdb_00002jxp

Solution NMR structure of uncharacterized lipoprotein B from Nitrosomonas europaea. Northeast Structural Genomics target NeR45A

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
2	2D 1H-13C HSQC	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
3	3D CBCA(CO)NH	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
4	3D HNCACB	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
5	3D HNCA	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
6	3D HN(CO)CA	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
7	3D HBHA(CO)NH	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
8	3D SIMULTANEOUS 15N-13C NOESY	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
9	3D 1H-13C NOESY	0.86 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	100% D2O	0.1	6.5	ambient	298
10	3D HCCH-COSY	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
11	3D HCCH-TOCSY	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
12	3D CCH-TOCSY	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
13	2D 1H-13C HSQC	1.3 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
14	3D HNCO	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298
15	3D HNCACO	1 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide	95% H2O/5% D2O	0.1	6.5	ambient	298

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

NMR Refinement
Method	Details	Software
torsion angle dynamics		CYANA

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

Additional NMR Experimental Information

Details

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 98.9%, SIDECHAIN 86.6%, AROMATIC (SC) 78.4%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2279 NOE. MAX NOE VIOLATION 0.46 A (1 MODEL). 22 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELICES: (26-38, 114-117, 120-143), BETA STRANDS: (42-44, 16-20, 52-65, 76-89, 100-108, 94-96, 68-69, 73-74) FOR [S(PHI)+S(PSI)] > 1.8. RMSD 0.7 BB, 1.3 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 90.4/9.5/0.1/0.0. PROCHECK (PSI-PHI): -0.34/-1.02 (RAW/Z), PROCHECK (ALL): -0.35/-2.07 (RAW/Z), MOLPROBITY CLASH: 20.44/-1.98 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.868, PRECISION: 0.871, F-MEASURE: 0.869, DP-SCORE: 0.706.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	backbone chemical shift assignment	AutoAssign	2.4	Zimmerman, Moseley, Kulikowski and Montelione
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
5	validation	PSVS	1.3	Bhattacharya and Montelione
6	data analysis	Sparky	3.112	Goddard
7	collection	TopSpin	1.3	Bruker Biospin
8	visualization	MOLMOL	2.2	Koradi, Billeter and Wuthrich
9	validation	RPF	2.1.1	Huang, Powers and Montelione
10	validation	Procheck		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss et al.
11	validation	MolProbity		Richardson
12	data analysis	XEASY		Bartels et al.