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BMRB: 30485

NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGG)

Authors

Assembly

Sp1 transcription factor duplex 5'-d(TGGGCGGGG)

Entity

1. Sp1 transcription factor duplex 5'-d(TGGGCGGGG), entity 1 (polymer, Thiol state: not present), 9 monomers, 2915.830 Da Detail

TGGGCGGGG

2. Sp1 transcription factor duplex 5'-d(TGGGCGGGG), entity 2 (polymer, Thiol state: not present), 9 monomers, 2684.700 Da Detail

CCCCGCCCA

Total weight

5600.5303 Da

Max. entity weight

2915.83 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 74.3 %, Completeness (bb): 84.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	74.3 % (133 of 179)	74.3 % (133 of 179)
Suger, PO4	84.9 % (107 of 126)	84.9 % (107 of 126)
Nucleobase	49.1 % (26 of 53)	49.1 % (26 of 53)
Aromatic	72.2 % (26 of 36)	72.2 % (26 of 36)
Methyl	0.0 % (0 of 1)	0.0 % (0 of 1)

1. entity 1

TGGGCGGGG

2. entity 2

CCCCGCCCA

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 900 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DNA	natural abundance	900 uM
7	DNA	natural abundance	900 uM
8	sodium chloride	natural abundance	25 mM
9	Na Phosphate	natural abundance	5 mM
10	EDTA	natural abundance	0.5 mM

Release date

2018-07-08

Citation

An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences
Davis, E.V., Hennig, M., Arya, D.P.

Experiments performed 6 experiments Detail

1 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

5 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 900 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DNA	natural abundance	900 uM
7	DNA	natural abundance	900 uM
8	sodium chloride	natural abundance	25 mM
9	Na Phosphate	natural abundance	5 mM
10	EDTA	natural abundance	0.5 mM

6 2D ECOSY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.0 mM
2	DNA	natural abundance	1.0 mM
3	sodium chloride	natural abundance	25 mM
4	Na Phosphate	natural abundance	5 mM
5	EDTA	natural abundance	0.5 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30485_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30485_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	133		100.0 (chain: 1, length: 9), 100.0 (chain: 2, length: 9)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 9, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 133
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	62	73.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	52	82.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	10	47.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	71	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	55	87.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	16	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	2	66.7

Keywords DNA, Sp1 Consensus Sequence

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Found 1 Document (0.255 seconds)

BMRB: 30485

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

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Sample

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Sample

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Chemical shift validation 4 contents Detail