8BGF | pdb_00008bgf

NMR solution structure of the N-terminal RRM and flanking linker regions of Polypyrimidine tract binding protein 1 using the CYANA CONSENSUS method.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D 1H-15N NOESY	0.8 mM [U-13C,15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 900
2	3D 1H-13C NOESY	0.8 mM [U-13C,15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 900
3	15N T1-relaxation-15HSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	313	Bruker AVANCE 700
4	15N T2-relaxation-T1rho-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	313	Bruker AVANCE 700
5	{1H}15N-NOE-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	313	Bruker AVANCE 700
6	relaxation-compensated IzNz Rex HSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 750
7	15N T2-relaxation-dispersion CPMG-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 750
8	15N T2-relaxation-dispersion-CPMG-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 900
17	15N T2-relaxation-dispersion-CPMG-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	293	Bruker AVANCE 750
18	cross-correlated DD/CSA relaxation-15NHSQC	0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride	90% H2O/10% D2O	33.3 mM	6.5	1 atm	298	Bruker AVANCE 750

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	900
2	Bruker	AVANCE	750
3	Bruker	AVANCE	700
4	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
torsion angle dynamics	The structure was calculated using the CONSENSUS protocol of CYANA due better sample the conformational space consistent with the input data. Unlike in traditional CYANA structure calculations, in CONSENSUS structure calculations the constraint list includes ambiguous restraints. There is no refinement protocol for NMR structures using programs which have realistic energy potentials for ambiguous restraints. In addition the structure includes a highly dynamic structural element (alpha3). Therefore no standard refinement was performed.	CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	2000
Conformers Submitted Total Number	20
Representative Model	1 (target function)

Additional NMR Experimental Information

Details

STRUCTURE WAS CALCULATED USING CONSENSUS METHOD (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS WERE PERFORMED AND A SET OF CONSTRAINTS CONSISTENT AMONG 60% OF THE ENSEMBLES WAS COMBINED FOR A FINAL CONSENSUS CALCULATION TO GENERATE THIS ENSEMBLE THE PROTEIN CONTAINS A DYNAMIC REGION WITH RESIDUAL STRUCTURE. DUE TO THE AMBIGUOUS NATURE OF THE CONSTRAINTS AND THE DYNAMIC REGION NO ENERGY REFINEMENT WAS PERFORMED

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure calculation	CYANA	3.97beta	Guntert & Buchner
2	refinement	CYANA	3.97beta	Guntert & Buchner
3	processing	TopSpin	3	Bruker Biospin
4	chemical shift assignment	CARA	1.9.1.7	Keller and Wuthrich
5	peak picking	CYANA	3.97beta	Wurz & Guntert