2LVC | pdb_00002lvc

Solution NMR Structure of Ig like domain (805-892) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578K

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
2	2D 1H-13C (CT-27 ms) HSQC	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
3	3D HNCO	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
4	3D CBCA(CO)NH	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
5	3D HNCACB	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
6	3D HN(CA)CO	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
7	3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
8	2D 1H-13C (CT-28 ms) HSQC	1.0 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
9	2D 1H-13C (CT-56 ms) HSQC	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
10	2D 1H-13C (CT-42 ms) HSQC	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
11	3D C(CO)NH	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
12	3D HCCH-TOCSY	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
13	3D HBHA(CO)NH	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
14	3D H(CCO)NH	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
15	3D HCCH-COSY (Aliphatic)	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
16	3D HCCH-COSY (Aromatic)	1.0 mM [U-100% 13C; U-100% 15N] HR8578K.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
17	2D 1H-15N HSQC J-mod	0.6 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 12.5 mg/mL PF1 Phage	80% H2O/20% D2O		6.5	ambient	298
18	2D 1H-15N HSQC J-mod	0.6 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 4 % PEG	80% H2O/20% D2O		6.5	ambient	298
19	2D 1H-15N HSQC J-mod	1.0 mM [U-5% 13C; U-100% 15N] HR8578K.010, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	750
3	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing	STRUCTURE DETERMINATION WAS PERFORMED BY CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSENSUS PEAK ASSIGNMENTS GENERATED FROM THESE PARALLEL RUNS WERE SELECTED AND USED FOR FURTHER REFINEMENT WITH CYANA, THE RDC CONSTRAINTS WERE ADDED AT LATER STAGES. A TOTAL OF 20 CONFORMERS OUT OF 100 CONFORMERS WITH THE LOWEST TARGET FUNCTION WERE SELECTED FOR REFINEMENT WITH CNS USING CNS WATER BATH REFINEMENT	CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
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		Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
3	geometry optimization	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
4	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
5	geometry optimization	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
6	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
7	data analysis	AutoStructure	2.1	Huang, Tejero, Powers and Montelione
8	refinement	AutoStructure	2.1	Huang, Tejero, Powers and Montelione
9	data analysis	AutoAssign	2.1	Zimmerman, Moseley, Kulikowski and Montelione
10	chemical shift assignment	AutoAssign	2.1	Zimmerman, Moseley, Kulikowski and Montelione
11	peak picking	CARA	1.8.4	Keller and Wuthrich
12	data analysis	CARA	1.8.4	Keller and Wuthrich
13	data analysis	XEASY		Bartels et al.
14	peak picking	XEASY		Bartels et al.
15	chemical shift assignment	XEASY		Bartels et al.
16	data analysis	CSI		Wishart, D.S. and B.D. Sykes.
17	collection	VnmrJ		Varian
18	processing	PROSA		Guntert
19	geometry optimization	TALOS+		Shen, Cornilescu, Delaglio and Bax
20	geometry optimization	PALES		Zweckstetter, Bax
21	structure validation	PSVS		Bhattacharya, Montelione

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 2LVC | pdb_00002lvc

Solution NMR Structure of Ig like domain (805-892) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578K

2LVC | pdb_00002lvc