BMRBj - BMREntryMaster

Found 1 Document (0.246 seconds)

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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.246 seconds)

BMRB: 30485

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail