6CC9 | pdb_00006cc9

NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-13C HMQC, 1H-15N TROSY	0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC	90% H2O/10% D2O	100 mM NaCl mM	7.4	ambient atm	298	Bruker AVANCE 800
2	2D 1H-13C HMQC, 1H-15N TROSY	0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 1 mM Cmpd2, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC	90% H2O/10% D2O	100 mM NaCl mM	7.4	ambient atm	298	Bruker AVANCE 800
3	3D_15N-separated_NOESY	0.2 mM [U-15N] GTPase KRas isoform b, 1 mM Cmpd2, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP	90% H2O/10% D2O	100 mM NaCl mM	7.4	ambient atm	298	Bruker AVANCE 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing		CNS

NMR Ensemble Information
Conformer Selection Criteria	10 structures for lowest energy
Conformers Calculated Total Number	3000
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	HADDOCK modelling consists of (I) rigid-body docking, (II) a semi-flexible refinement stage, and (III) final refinement in explicit solvent (final gentle water). The starting structure is 2MSE. Distance restraints are based on PRE and NOE.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS		Brunger A. T. et.al.
2	structure calculation	HADDOCK		Bonvin
3	chemical shift assignment	SPARKY-NMRFAM		Goddard. et. al.