7K7F

Solution Structure of the Corynebacterium diphtheriae SpaA Pilin-Signal Peptide Complex

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE NEO 800
2	3D_(F1)_13C,15N-filtered_(F2)_15N-edited NOESY-HSQC	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
3	2D 1H-15N HSQC	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
4	2D 1H-13C HSQC	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
5	2D 1H-13C HSQC aromatic	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
6	3D HNCACB	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
7	1H-15N heteronoe	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
8	3D CBCA(CO)NH	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
9	T2/R2 relaxation	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
10	T1/R1 relaxation	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
11	3D HN(CA)CO	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
12	3D HNCA	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
13	3D HNCO	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
14	3D HCCH-COSY	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
17	3D HNHA	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
18	3D HBHA(CO)NH	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE NEO 800
19	3D 1H-15N TOCSY	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE NEO 800
20	3D H(CCO)NH	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
21	2D (F1,F2) 13C-filtered NOESY	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
22	2D (F1) 13C,15N-filtered TOCSY	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
24	3D_13C-separated_NOESY_aliphatic_D2O	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
23	3D_(F1)_13C,15N-filtered_(F2)_13C-edited NOESY-HSQC	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
25	3D_13C-separated_NOESY_aromatic_D2O	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	100% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600
26	3D_13C-separated_NOESY_aliphatic_H2O	1.2 mM [U-13C; U-15N] SpaA backbone pilin for protein, 1.2 mM SpaA sorting signal for peptide, 50 mM NaH2PO4, 100 mM NaCl, 0.01 % NaN3	92% H2O, 8% D2O	100mM NaCl mM	6.0	ambient	298	Bruker AVANCE III HD 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	600
2	Bruker	AVANCE NEO	800

NMR Refinement
Method	Details	Software
simulated annealing	NOE restraints refined in XIPP, structures were calculated with a simulated annealing protocol using XPLOR-NIH	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR NIH	2.37	Schwieters, Kuszewski, Tjandra and Clore
2	structure calculation	X-PLOR NIH	2.37	Schwieters, Kuszewski, Tjandra and Clore
3	chemical shift assignment	Xipp	1.19	Dan Garrett
4	peak picking	Xipp	1.19	Dan Garrett
5	structure calculation	UNIO		Torsten Herrmann
6	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7	collection	TopSpin		Bruker Biospin
8	data analysis	NMRFAM-SPARKY		National Magnetic Resonance Facility at Madison (Wisconsin)
9	peak picking	CARA		Keller and Wuthrich
10	geometry optimization	TALOS-N		Cornilescu, Delaglio and Bax
11	refinement	MOLMOL		Koradi, Billeter and Wuthrich
12	refinement	PROCHECK / PROCHECK-NMR		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

7K7F

Solution Structure of the Corynebacterium diphtheriae SpaA Pilin-Signal Peptide Complex