6GVT | pdb_00006gvt

Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules

SOLUTION NMR - SOLID-STATE 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] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
2	3D HN(CO)CA	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
3	3D HNCACB	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
4	3D CBCA(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
5	3D HNCO	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
6	3D C(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
7	3D H(CCO)NH	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
8	3D 1H-15N NOESY	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III HD 900
9	3D 1H-13C NOESY aliphatic	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III HD 900
10	3D 1H-13C NOESY aromatic	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III HD 900
11	3D 1H-13C NOESY aromatic	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III HD 900
12	3D 1H-15N NOESY	1.0 mM [U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III HD 900
13	2D 1H-1H NOESY	1.0 mM pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
14	2D 1H-1H TOCSY	1.0 mM pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
15	2D 1H-1H NOESY	1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III 700
16	2D 1H-1H TOCSY	1.0 mM [U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III 700
17	2D 1H-13C HSQC aromatic	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 600
18	2D 1H-13C HSQC aliphatic	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 600
19	2D-F1fF2f-NOESY	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
20	2D-F2f-NOESY	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
21	3D-13C-aliphatic-HfilteredHedited-NOESY	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
22	3D-13C-aliphatic-HfilteredHedited-NOESY	0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	100% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 700
23	3D-13C-aromatic-HfilteredHedited-NOESY	1.0 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	100% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III 700
24	3D-13C-aromatic-HfilteredHedited-NOESY	1.0 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	100% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III 700
25	2D-imino-NOESY	1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	278	Bruker AVANCE III 700
26	2D-natural-abundance-Chsqc	1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III 600
27	DARR	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 850
28	NCX(R)	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 850
29	NCX(W)	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 850
30	CHHP	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 500
31	NHHP	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 500
32	31P CPMAS	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 500
33	31P-31P-DARR	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 500
34	31P CPMAS	4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	278	Bruker AVANCE III 850
35	2D 1H-15N HSQC	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	50 mM NaCl 10mM MgCl2 mM	7.0	ambient atm	298	Bruker AVANCE III HD 900
36	2D 1H-15N HSQC	1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium	90% H2O/10% D2O	100 mM NaCl 10mM MgCl2 mM	5.0	ambient atm	298	Bruker AVANCE III HD 900

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	900
2	Bruker	AVANCE III	700
3	Bruker	AVANCE III	600
4	Bruker	AVANCE III	850
5	Bruker	AVANCE III	500

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	structure calculation	CYANA		Guntert P.
2	data analysis	Sparky		Goddard
3	chemical shift assignment	MARS		Jung and Zweckstetter
4	peak picking	CANDID		Herrmann, Guntert and Wuthrich
5	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
6	processing	TopSpin		Bruker Biospin
7	chemical shift assignment	Sparky		Goddard
8	data analysis	CcpNmr Analysis		CCPN
9	collection	TopSpin		Bruker Biospin