2M72 | pdb_00002m72

Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	15N HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
2	15N NOESY-HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
3	13C HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	100% D2O	10	4.5	1 atm	298
4	aromatic 13C HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	100% D2O	10	4.5	1 atm	298
5	13C NOESY-HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	100% D2O	10	4.5	1 atm	298
6	13C aromatic NOESY-HSQC	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	100% D2O	10	4.5	1 atm	298
7	HNCO	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
8	HNCACO	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
9	HNCA	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
10	HNCOCA	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
11	HNCACB	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298
12	CBCACONH	10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA	90% H2O/10% D2O	10	4.5	1 atm	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Bruker	AVANCE	700

NMR Refinement
Method	Details	Software
simulating annealing	Refinement in a box of water using XPLOR-NIH	CNS

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

Additional NMR Experimental Information
Details	All 3Ds were collected as NUS (30%) using the MDDNMR approach

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure calcuation	CNS	1.21	Brunger A. T. et.al.
2	structure calcuation	ARIA	2.3	Linge, O'Donoghue and Nilges
3	structure solution	X-PLOR NIH	2.32	Schwieters, Kuszewski, Tjandra and Clore
4	refinement	X-PLOR NIH	2.32	Schwieters, Kuszewski, Tjandra and Clore
5	data analysis	CCPN_Analysis	2.2	CCPN
6	chemical shift assignment	CCPN_Analysis	2.2	CCPN
7	collection	MddNMR	2.2	(MDDNMR) Orekhov, Jaravine, Kazimierczuk
8	processing	MddNMR	2.2	(MDDNMR) Orekhov, Jaravine, Kazimierczuk
9	collection	MDDGUI		(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith
10	processing	MDDGUI		(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith
11	processing	NMRPipe	7.5	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
12	data analysis	SideR		Hansen
13	collection	VnmrJ	2.2D	Varian
14	collection	TopSpin	2.1	Bruker Biospin
15	data analysis	MolProbity		Richardson
16	refinement	CNS

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.