2KPM

Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
2	2D 1H-13C HSQC	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
3	3D HCCH-TOCSY	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
4	3D HCCH-COSY	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
5	3D CCH-TOCSY	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
6	3D HNCO	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
7	3D HNCACB	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
8	3D HBHA(CO)NH	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
9	3D CBCA(CO)NH	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
10	3D 1H-15N NOESY	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
11	3D 1H-13C NOESY	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
12	3D HN(CA)CO	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
13	3D HNCA	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
14	het-NOE	0.9 mM [U-5% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
15	T1-pseudo2D	0.9 mM [U-5% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
16	T2CPMG-pseudo2D	0.9 mM [U-5% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
17	high-resC13-HSQC	0.9 mM [U-5% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
18	1D presat referencing	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
19	1D presat referencing	0.957 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298

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

NMR Refinement
Method	Details	Software
torsion angle dynamics, molecular dynamics	Iterative noesy assignment followed by torsion angle dynamics in CYANA-3.0, STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 86.63%, SIDECHAIN 76.84%, AROMATIC (SC) 100%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2412 NOE, 230 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 8.1 DEG. 3 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 19-98. SECONDARY STRUCTURE - ALPHA HELICES: 23-32, 42-52, 66-72. BETA STRANDS: 40-41, 90-96, 77-83. RMSD(ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. RAMA. DISTRIBUTION (MOLPROBITY): 97/3/0/0 PROCHECK (PSI-PHI): -0.12/-0.16 (RAW/Z), PROCHECK (ALL): 0.04/0.24 (RAW/Z), MOLPROBITY CLASH: 9.92/-0.18 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.91, PRECISION: 0.93, F-MEASURE: 0.92, DP-SCORE: 0.79.	CNS

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 AND BY NMR. T1/T2(CPMG). CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	Sparky	3.112	Goddard
5	chemical shift assignment	PINE		Bahrami, Markley, Assadi, and Eghbalnia
6	geometry optimization	TALOS	+	Shen,Cornilescu, Delaglio and Bax
7	validation	PSVS	1.3	Bhattacharya and Montelione
8	collection	TopSpin	2.1	Bruker Biospin
9	visualization	PyMOL	1.2	delano scientific

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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2KPM

Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A