7Q4L | pdb_00007q4l

The solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA

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	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
2	2D 1H-13C HSQC	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
3	3D 1H-15N NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
4	3D HNCO TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
5	3D HN(CA)CO TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
6	3D 1H-15N NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
7	3D HN(CO)CACB TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
8	3D HNCACB TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
9	3D HN(CO)CA TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
10	3D HNCA TROSY	0.8 mM fractionally deuterated, 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
11	2D 1H-13C HSQC	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
12	2D F1 filtered, F2 filtered NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
13	2D F2 filtered NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
14	2D NOESY	0.8 mM hsDnd1 RRM12, 0.8 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
15	2D TOCSY	0.8 mM hsDnd1 RRM12, 0.8 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 600
16	3D HCCH-COSY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 600
17	3D HCCH-TOCSY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 600
18	3D HCCH-TOCSY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 600
19	3D 1H-13C-HSQC-aromatic-NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
20	3D 1H-13C-HMQC-NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
21	2D 1H-13C HSQC	0.8 mM hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled CU*UA*UU*UG* RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
22	2D 1H-13C HSQC	0.8 mM hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled C*UU*AU*UU*G RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
23	2D F2 filtered NOESY	0.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled CU*UA*UU*UG* RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
24	2D F2 filtered NOESY	0.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled C*UU*AU*UU*G RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
25	2D F1 filtered, F2 filtered NOESY	0.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled CU*UA*UU*UG* RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
26	2D F1 filtered, F2 filtered NOESY	0.8 mM 13C15N hsDnd1 RRM12, 0.8 mM selectively 13C ribose-labeled C*UU*AU*UU*G RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
27	2D 1H-1H TOCSY	0.8 mM hsDnd1 RRM12, 0.8 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
28	3D F3 filtered, F2 edited 13C HMQC-NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
29	2D 13C F2 filtered 2D NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
30	2D 13C F1 filtered, F2 filtered NOESY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	100% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE 900
31	2D 1H-15N TROSY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT, 4.2 % C12E5 polyethylene glycol / hexanol	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700
32	2D 1H-15N TROSY	0.8 mM 13C,15N-labeled hsDnd1 RRM12, 0.9 mM RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), 100 mM KHPO4/ KH2PO4 pH 6.6, 1 mM DTT	95% H2O/5% D2O	100 mM	6.6	AMBIENT atm	298	Bruker AVANCE III 700

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

NMR Refinement
Method	Details	Software
torsion angle dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations and lowest energy
Conformers Calculated Total Number	50
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	2.1	Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	NMRFAM-SPARKY	1.1412	Lee W, Tonelli M, Markley JL
4	structure calculation	CYANA	3.98	Guntert, Mumenthaler and Wuthrich
5	structure calculation	Amber	12	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
6	peak picking	ATNOS	3.1	ATNOS-CANDID
7	chemical shift assignment	Sparky		Goddard
8	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman