Experiment: 2MA4

Solution NMR Structure of yahO protein from Salmonella typhimurium, Northeast Structural Genomics Consortium (NESG) Target StR106

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] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
2	2D 1H-13C HSQC aliphatic	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
3	3D HNCO	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
4	(4,3)D GFT CABCA(CO)NHN	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
5	(4,3)D GFT HNHNCABCA	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
6	(4,3)D GFT HABCAB(CO)NHN	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
7	3D 1H-15N,13C NOESY	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
8	(4,3)D GFT HCCH-COSY aliphatic	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
9	3D (H)CCH-COSY aromatic	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
10	3D (H)CCH-TOCSY aliphatic	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
11	2D 1H-13C HSQC aromatic	1.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
12	2D 1H-13C HSQC methyl	1 mM [5% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	90% H2O/10% D2O		4.5	ambient	298
13	2D 1H-15N HSQC	0.3 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS	100% D2O		4.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
2	Varian	INOVA	750

NMR Refinement
Method	Details	Software
simulated annealing	STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD	CNS

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	refinement	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
2	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
3	geometry optimization	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
4	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
5	structure calculation	AS-DP	1.0	Huang, Tejero, Powers and Montelione
6	refinement	AS-DP	1.0	Huang, Tejero, Powers and Montelione
7	data analysis	XEASY	1.3.13	Bartels et al.
8	peak picking	XEASY	1.3.13	Bartels et al.
9	chemical shift assignment	XEASY	1.3.13	Bartels et al.
10	data analysis	XEASY	1.3.13	Bartels et al.
11	data analysis	XEASY	1.3.13	Keller and Wuthrich
12	peak picking	XEASY	1.3.13	Keller and Wuthrich
13	chemical shift assignment	XEASY	1.3.13	Keller and Wuthrich
14	data analysis	XEASY	1.3.13	Keller and Wuthrich
15	collection	VnmrJ	2.2D	Varian
16	geometry optimization	TALOS+		Shen, Cornilescu, Delaglio and Bax
17	structure validation	PSVS	1.4	Bhattacharya, Montelione
18	data analysis,peak picking,chemical shift assignment	XEASY	1.3.13	Bartels et al.
19	data analysis	XEASY	1.3.13	Bartels et al.
20	data analysis,peak picking,chemical shift assignment	XEASY	1.3.13	Keller and Wuthrich
21	data analysis	XEASY	1.3.13	Keller and Wuthrich
22	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
23	processing	PROSA	6.4	Guntert
24	data analysis	DYANA	1.5	Guntert, Braun and Wuthrich
25	data analysis	UBNMR	1.0	Shen

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

2MA4 | pdb_00002ma4

Solution NMR Structure of yahO protein from Salmonella typhimurium, Northeast Structural Genomics Consortium (NESG) Target StR106