2GLO | pdb_00002glo

Solution structure of the Brinker DNA binding domain in complex with the omb enhancer

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	1mM brkDBD U-15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298
2	3D_13C-separated_NOESY	1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298
3	3D_dq-HNHA	1mM brkDBD U-15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298
4	3D_dq-HAHB, 2D_HNCG, 2D_HN(CO)CG	1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298
5	2D_13C-selected/12C,14N-selected NOESY	1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298
6	DSSE, J-modulated-13C-HSQC	0.35mM brkDBD U-13C/15N, 0.35mM DNA omb12 NA; 10mM NaCl; 20mM potassium phosphate; 2mM DTT; 0.02% NaN3; 25mg/ml Pf1-phages; 95% H2O, 5% D2O	95% H2O/5% D2O	10mM NaCl	5.8	ambient	298

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

NMR Refinement
Method	Details	Software
torsion angle dynamics; distance geometry	The structures are based on 1279 NOE-derived distance constraints, 21 Ambiguous Interaction Restraints, 21 distance restraints from hydrogen bonds, 92 RDC restraints, 30 dihedral angle restraints, 56 J-coupling constant restraints.	XwinNMR

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)

Additional NMR Experimental Information
Details	This structure was determined using standard 2D and 3D heteronuclear techniques and 12C/14N-filtered-NOESY experiments for DNA assignment and intermolecular NOE contacts

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.6	Bruker
2	processing	NMRPipe	2.2	Delaglio
3	data analysis	PIPP	4.3.2	Garrett
4	refinement	HADDOCK	1.2	Bonvin

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.