6K3K | pdb_00006k3k

Solution structure of APOBEC3G-CD2 with ssDNA, Product B

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCO	0.35 mM [U-100% 13C; U-100% 15N; U-80% 2H] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
2	3D HNCA	0.35 mM [U-100% 13C; U-100% 15N; U-80% 2H] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
3	3D HN(CO)CA	0.35 mM [U-100% 13C; U-100% 15N; U-80% 2H] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
4	3D HNCACB	0.35 mM [U-100% 13C; U-100% 15N; U-80% 2H] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
5	2D 1H-15N HSQC	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 800
6	2D 1H-13C HSQC aliphatic	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	100% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 800
7	2D 1H-13C HSQC aromatic	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	100% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 800
8	3D 1H-13C NOESY aliphatic	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	100% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 900
9	3D 1H-13C NOESY aromatic	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	100% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 900
10	3D 1H-15N NOESY	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 900
15	3D HCCH-TOCSY	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
14	3D 1H-15N TOCSY	0.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Bruker AVANCE III 850
11	2D 1H-1H NOESY	1 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Varian UNITY 600
12	2D 1H-1H TOCSY	1 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Varian UNITY 600
13	2D DQF-COSY	1 mM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 50 uM ZINC ION	90% H2O/10% D2O	150 mM	7.5	1 atm	293	Varian UNITY 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	800
2	Bruker	AVANCE III	850
3	Bruker	AVANCE III	900
4	Varian	UNITY	600

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (target function)

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