6GVU | pdb_00006gvu

NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCA	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
2	3D HN(CO)CA	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
3	3D HNCACB	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
4	3D CBCA(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
5	3D C(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 600
6	3D H(CCO)NH	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 600
7	3D 1H-15N NOESY	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III HD 900
8	3D 1H-13C NOESY aliphatic	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III HD 900
9	3D 1H-13C NOESY aromatic	1.0 mM [U-99% 13C; U-99% 15N] DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III HD 900
10	3D 1H-13C NOESY aromatic	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
11	2D 1H-15N HSQC	1.1 mM [U-99% 15N] DNA-bound helix bundle domain, 1.1 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
12	2D 1H-15N HSQC	1.1 mM [U-99% 15N] DNA-bound helix bundle domain, 1.1 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III 700
13	2D 1H-15N HSQC	1.1 mM [U-99% 15N] DNA-bound helix bundle domain, 1.1 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	50mM NaCl mM	7.0	ambient atm	298	Bruker AVANCE III 700
14	3D 1H-15N NOESY	1.1 mM [U-99% 15N] DNA-bound helix bundle domain, 1.1 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III HD 900
15	3D 1H-15N NOESY	1.1 mM [U-99% 15N] DNA-bound helix bundle domain, 1.1 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	50mM NaCl mM	7.0	ambient atm	298	Bruker AVANCE III 700
16	2D 1H-1H NOESY	1.0 mM DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
17	2D 1H-1H NOESY	1.0 mM DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III 700
18	2D 1H-1H TOCSY	1.0 mM DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
19	2D 1H-1H TOCSY	1.0 mM DNA-bound helix bundle domain, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	90% H2O/10% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III 700
20	2D-F1fF2f-NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
21	2D-F2f-NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
22	3D 13C-aliphatic Hfiltered-Hedited NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
23	3D 13C-aromatic Hfiltered-Hedited NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	323	Bruker AVANCE III 700
24	3D 13C-aliphatic Hfiltered-Hedited NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III 700
25	3D 13C-aromatic Hfiltered-Hedited NOESY	0.7 mM [U-100% 13C] DNA-bound helix bundle domain, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	100% D2O	100mM NaCl mM	5.5	ambient atm	298	Bruker AVANCE III 700

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	900
2	Bruker	AVANCE III	700
3	Bruker	AVANCE III	600

NMR Refinement
Method	Details	Software
simulated annealing		Amber

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	data analysis	Sparky		Goddard
2	peak picking	CANDID		Herrmann, Guntert and Wuthrich
3	chemical shift assignment	Sparky		Goddard
4	collection	TopSpin		Bruker Biospin
5	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
6	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman