2N7J | pdb_00002n7j

Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	ARTSY	2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3	95% H2O/5% D2O	0.05	6.5	ambient	293
2	ARTSY	2.5 mM [U-13C; U-15N; U-2H] wild-type GB3	95% H2O/5% D2O	0.05	6.5	ambient	293
3	ARTSY	0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6	95% H2O/5% D2O	0.05	6.5	ambient	293
4	ARTSY	0.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6	95% H2O/5% D2O	0.05	6.5	ambient	293
5	ARTSY	1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K	95% H2O/5% D2O	0.05	6.5	ambient	293
6	ARTSY	1.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K	95% H2O/5% D2O	0.05	6.5	ambient	293
7	ARTSY	2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E	95% H2O/5% D2O	0.05	6.5	ambient	293
8	ARTSY	2.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E	95% H2O/5% D2O	0.05	6.5	ambient	293
9	CT-HN(COCA)CB	2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3	95% H2O/5% D2O	0.05	6.5	ambient	293
10	CT-HN(COCA)CB	0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6	95% H2O/5% D2O	0.05	6.5	ambient	293
11	CT-HN(COCA)CB	1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K	95% H2O/5% D2O	0.05	6.5	ambient	293
12	CT-HN(COCA)CB	2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E	95% H2O/5% D2O	0.05	6.5	ambient	293
13	1H-13C HSQC	2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3	100% D2O	0.05	6.5	ambient	293
14	1H-13C HSQC	0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6	100% D2O	0.05	6.5	ambient	293
15	1H-13C HSQC	1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K	100% D2O	0.05	6.5	ambient	293
16	1H-13C HSQC	2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E	100% D2O	0.05	6.5	ambient	293
17	1H-13C CT-HSQC	2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3	100% D2O	0.05	6.5	ambient	293
18	1H-13C CT-HSQC	0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6	100% D2O	0.05	6.5	ambient	293
19	1H-13C CT-HSQC	1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K	100% D2O	0.05	6.5	ambient	293
20	1H-13C CT-HSQC	2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E	100% D2O	0.05	6.5	ambient	293
21	DEPT-filtered 1H-13C CT-HSQC	2.5 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K	100% D2O	0.05	6.5	ambient	293
22	DEPT-filtered 1H-13C CT-HSQC	0.9 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E-CHis6	100% D2O	0.05	6.5	ambient	293
23	DEPT-filtered 1H-13C CT-HSQC	1.3 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K	100% D2O	0.05	6.5	ambient	293
24	DEPT-filtered 1H-13C CT-HSQC	2.0 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E	100% D2O	0.05	6.5	ambient	293
25	HN(CO)CA	2.5 mM [U-13C; U-15N; U-2H] wild-type GB3	95% H2O/5% D2O	0.05	6.5	ambient	293
26	HN(CO)CA	0.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6	95% H2O/5% D2O	0.05	6.5	ambient	293
27	HN(CO)CA	1.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K	95% H2O/5% D2O	0.05	6.5	ambient	293
28	HN(CO)CA	2.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E	95% H2O/5% D2O	0.05	6.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600
2	Bruker	AVANCE III	900

NMR Refinement
Method	Details	Software
simulated annealing	STRUCTURES WERE OBTAINED BY A SINGLE-CONFORMER SIMULATED ANNEALING REFINEMENT WITH VARIABLE ALIGNMENT TENSORS AGAINST AN EXTENSIVE SET OF BACKBONE AND CA-CB RDCS IN MULTIPLE ALIGNMENT MEDIA, J-COUPLINGS INCLUDING HN-HA, C'-C', AND THROUGH HYDROGEN BOND N-C', AND A BACKBONE-BACKBONE HYDROGEN BONDING DATABASE-DERIVED POTENTIAL OF MEAN FORCE. BACKBONE GEOMETRIES RESULTING FROM THIS STEP WERE KEPT FIXED UP TO CB ATOMS AND CHI1 TORSION ANGLES WERE RANDOMLY SELECTED TO SAMPLE THE DISTRIBUTIONS DERIVED FROM THE ANALYSIS OF AN EXTENSIVE DATASET OF CB-CG AND CB-HB RDCS IN 6 ALIGNMENT MEDIA. CLASHING WAS MINIMIZED BY RANDOMLY SAMPLING CHI2, CHI3 AND CHI4 TORSION ANGLES SELECTED FROM THE KINEMAGE DATABASE. MODELS 2-20 SHOWING MINIMAL CLASHING WERE THEN SELECTED FOR DEPOSITION.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	structures with favorable non-bond energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (sidechain conformers in their most populated conformations)

Additional NMR Experimental Information
Details	MODEL 1 SHOWS THE SIDECHAIN CONFORMERS IN THEIR MOST POPULATED CONFORMATIONS. MODELS 2-20 SHOW THE STATISTICAL DISTRIBUTION OF SIDECHAIN CONFORMERS CONSISTENT WITH THE SIDECHAIN RDC DATA. NOTE THAT EXCEPT FOR RESIDUES POPULATING A SINGLE NARROWLY DISTRIBUTED RANGE OF CHI1 VALUES, SIDECHAIN RDCS ARE INCONSISTENT WITH ANY OF THE INDIVIDUAL MODELS.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	data analysis	Sparky		Goddard
3	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore