2L74 | pdb_00002l74

Solution structure of the PilZ domain protein PA4608 complex with c-di-GMP identifies charge clustering as molecular readout

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
2	2D 1H-13C HSQC	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
3	3D HNCO	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
4	3D HNCA	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
5	3D HNCACB	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
6	3D HBHA(CO)NH	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
7	3D H(CCO)NH	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
8	3D HCCH-TOCSY	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
9	3D HCCH-TOCSY (Ribose)	250 mM sodium chloride-10; 10 mM TRIS-11; 0.01 % sodium azide-12; 100% D2O	100% D2O		6.7	ambient	293
10	3D HCCH-COSY (Ribose)	250 mM sodium chloride-10; 10 mM TRIS-11; 0.01 % sodium azide-12; 100% D2O	100% D2O		6.7	ambient	303
11	HAHB	250 mM sodium chloride-7; 10 mM TRIS-8; 0.01 % sodium azide-9; 100% D2O	100% D2O		6.7	ambient	293
12	HAHB (Ribose)	250 mM sodium chloride-10; 10 mM TRIS-11; 0.01 % sodium azide-12; 100% D2O	100% D2O		6.7	ambient	293
13	HAHB (Ribose)	250 mM sodium chloride-13; 10 mM TRIS-14; 0.01 % sodium azide-15	93% H2O/7% D2O		6.7	ambient	293
14	13C-{13Cg}spin-echo difference H-15N HSQC	250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
15	15N-{13Cg} spin-echo diference H-15N HAQC	250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
16	Methyl C	250 mM sodium chloride-7; 10 mM TRIS-8; 0.01 % sodium azide-9; 100% D2O	100% D2O		6.7	ambient	293
17	Methyl N	250 mM sodium chloride-7; 10 mM TRIS-8; 0.01 % sodium azide-9; 100% D2O	100% D2O		6.7	ambient	293
18	3D 1H-15N ROESY	250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
19	3D 1H-15N NOESY	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
20	3D 1H-13C NOESY aliphatic	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
21	3D 1H-13C NOESY aromatic	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
22	3D 1H-13C NOESY(Ribose)	250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
23	4D 13C-13C NOESY	250 mM sodium chloride-7; 10 mM TRIS-8; 0.01 % sodium azide-9; 100% D2O	100% D2O		6.7	ambient	293
24	2D 1H-1H NOESY	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
25	2D 1H-1H NOESY (filtered against H bound to 13C, 15N)	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
26	IPAP 1H-15N HSQC	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
27	IPAP 1H-15N HSQC	250 mM sodium chloride-13; 10 mM TRIS-14; 0.01 % sodium azide-15	93% H2O/7% D2O		6.7	ambient	293
28	J-resolved ct 13C-HSQC	250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
29	J-resolved ct 13C-HSQC	250 mM sodium chloride-13; 10 mM TRIS-14; 0.01 % sodium azide-15	93% H2O/7% D2O		6.7	ambient	293
30	2D H-resolved 15N EXSY	250 mM sodium chloride-19; 10 mM TRIS-20; 0.01 % sodium azide-21; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
31	3D H-15N-15N EXSY	250 mM sodium chloride-19; 10 mM TRIS-20; 0.01 % sodium azide-21; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	313
32	IPAP 1H-15N HSQC	250 mM sodium chloride-4; 10 mM TRIS-5; 0.01 % sodium azide-6; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
33	IPAP 1H-15N HSQC	250 mM sodium chloride-22; 10 mM TRIS-23; 0.01 % sodium azide-24; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
34	2D 1H resolved 15N EXSY	250 mM sodium chloride-19; 10 mM TRIS-20; 0.01 % sodium azide-21; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	303
35	2D 1H-resolved 15N EXSY	250 mM sodium chloride-19; 10 mM TRIS-20; 0.01 % sodium azide-21; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	313
36	2D 1H-15N HSQC	250 mM sodium chloride-4; 10 mM TRIS-5; 0.01 % sodium azide-6; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
37	15N Relaxation	250 mM sodium chloride-4; 10 mM TRIS-5; 0.01 % sodium azide-6; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293
38	15N Relaxation	250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O	95% H2O/5% D2O		6.7	ambient	293

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

NMR Refinement
Method	Details	Software
simulated annealing		NMRPipe

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	peak picking	PIPP		Garrett
3	chemical shift assignment	Sparky		Goddard
4	structure solution	Sparky		Goddard
5	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	refinement	Sparky		Goddard