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BMRB: 30473

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

Authors

Assembly

Sp1 transcription factor duplex 5'-d(GGGGCGGGG)

Entity

1. Sp1 transcription factor duplex 5'-d(GGGGCGGGG), entity 1 (polymer, Thiol state: not present), 9 monomers, 2940.843 Da Detail

GGGGCGGGG

2. Sp1 transcription factor duplex 5'-d(GGGGCGGGG), entity 2 (polymer, Thiol state: not present), 9 monomers, 2660.675 Da Detail

CCCCGCCCC

Total weight

5601.518 Da

Max. entity weight

2940.843 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: 87.9 %, Completeness (bb): 86.8 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	87.9 % (174 of 198)	91.1 % (164 of 180)	55.6 % (10 of 18)
Suger, PO4	86.8 % (125 of 144)	91.3 % (115 of 126)	55.6 % (10 of 18)
Nucleobase	90.7 % (49 of 54)	90.7 % (49 of 54)
Aromatic	94.4 % (34 of 36)	94.4 % (34 of 36)

1. entity 1

GGGGCGGGG

2. entity 2

CCCCGCCCC

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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 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 680 uM DNA, 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	entity_1	natural abundance	680 uM
7	entity_2	natural abundance	680 uM
8	NaCl	natural abundance	25 mM
9	Na Phosphate	natural abundance	5.0 mM
10	EDTA	natural abundance	0.5 mM

Release date

2018-06-28

Citation

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

Experiments performed 8 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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 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 680 uM DNA, 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	entity_1	natural abundance	680 uM
7	entity_2	natural abundance	680 uM
8	NaCl	natural abundance	25 mM
9	Na Phosphate	natural abundance	5.0 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 NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 mM
5	EDTA	natural abundance	0.5 mM

7 2D PhCOSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 mM
5	EDTA	natural abundance	0.5 mM

8 2D PhTOCSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM DNA, 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	entity_2	natural abundance	1.0 mM
3	NaCl	natural abundance	25 mM
4	Na Phosphate	natural abundance	5.0 mM
5	EDTA	natural abundance	0.5 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30473_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	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr30473_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	244		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: Warning
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: 164
- ¹³C chemical shifts: 70
- ³¹P chemical shifts: 10

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C1'	85.527
1	DG	C3'	79.246
1	DG	C8	139.091
2	DG	C1'	84.467
2	DG	C3'	79.18
2	DG	C8	138.085
2	DG	P	-3.849
3	DG	C1'	84.364
3	DG	C3'	79.179
3	DG	C8	137.803
4	DG	C1'	84.629
4	DG	C3'	79.299
4	DG	C8	137.511
4	DG	P	-4.091
5	DC	C1'	86.351
5	DC	C3'	76.984
5	DC	C5	98.476
5	DC	C6	142.388
6	DG	C1'	84.247
6	DG	C3'	79.346
6	DG	C4'	87.259
6	DG	C8	138.382
6	DG	P	-3.885
7	DG	C1'	84.347
7	DG	C3'	79.126
7	DG	C8	137.892
8	DG	C1'	84.34
8	DG	C3'	78.841
8	DG	C8	137.856
9	DG	C1'	84.855
9	DG	C3'	72.786
9	DG	C4'	87.714
9	DG	C8	138.602
9	DG	P	-3.819

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	72	86.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	54	85.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	18	90.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Entity_assemble_ID: 2

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DC	C1'	88.202
1	DC	C3'	77.277
1	DC	C5	99.523
1	DC	C6	143.155
2	DC	C1'	87.041
2	DC	C3'	78.649
2	DC	C4'	86.315
2	DC	C5	98.997
2	DC	C6	143.415
2	DC	P	-4.058
3	DC	C1'	86.753
3	DC	C3'	78.392
3	DC	C5	99.173
3	DC	C6	143.364
3	DC	P	-3.972
4	DC	C1'	86.587
4	DC	C3'	77.309
4	DC	C4'	85.704
4	DC	C5	99.042
4	DC	C6	143.234
4	DC	P	-3.812
5	DG	C1'	84.481
5	DG	C3'	79.698
5	DG	C8	138.139
5	DG	P	-4.053
6	DC	C1'	86.747
6	DC	C3'	76.627
6	DC	C4'	85.581
6	DC	C5	98.353
6	DC	C6	142.308
7	DC	C1'	86.947
7	DC	C3'	76.019
7	DC	C4'	85.502
7	DC	C5	98.692
7	DC	C6	143.025
7	DC	P	-4.043
8	DC	C1'	86.986
8	DC	C3'	75.798
8	DC	C5	86.986
8	DC	C6	143.354
8	DC	P	-4.001
9	DC	C1'	87.279
9	DC	C3'	72.083
9	DC	C4'	87.074
9	DC	C5	99.096
9	DC	C6	144.18

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	92	94.8

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	61	96.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	31	91.2

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

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

Histogram of normalized assigned chemical shifts

Keywords DNA, Sp1 Consensus Sequence

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Found 1 Document (0.334 seconds)

BMRB: 30473

Sample #1

Sample #2

Experiments performed 8 experiments Detail

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Chemical shift validation 4 contents Detail