BMRBj - BMREntryMaster

Found 1 Document (0.314 seconds)

BMRB: 19572

2MFU

Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions.

Authors

Karsisiotis, A., Dillon, P., Webba da Silva, M.

Assembly

quadruplex d(TGGGTTTGGGTTGGGTTTGGG)

Entity

1. quadruplex d(TGGGTTTGGGTTGGGTTTGGG) (polymer, Thiol state: not present), 21 monomers, 6706.218 Da Detail

TGGGTTTGGG TTGGGTTTGG G

Formula weight

6706.218 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 73.7 %, Completeness (bb): 71.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	73.7 % (146 of 198)	73.7 % (146 of 198)
Suger, PO4	71.4 % (105 of 147)	71.4 % (105 of 147)
Nucleobase	80.4 % (41 of 51)	80.4 % (41 of 51)
Aromatic	76.2 % (32 of 42)	76.2 % (32 of 42)
Methyl	100.0 % (9 of 9)	100.0 % (9 of 9)

1. DNA

TGGGTTTGGG TTGGGTTTGG G

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	70 mM
4	H2O	natural abundance	93 %
5	D2O	[U-100% 2H]	7 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	70 mM
9	D2O	[U-100% 2H]	100 %

Release date

2014-10-26

Citation

In preparation
Karsisiotis, A., Dillon, P., Webba da Silva, M.
Not known

Experiments performed 6 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	70 mM
9	D2O	[U-100% 2H]	100 %

2 2D 1H-1H DQF-COSY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	70 mM
9	D2O	[U-100% 2H]	100 %

3 2D 1H-1H NOESY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	70 mM
9	D2O	[U-100% 2H]	100 %

4 2D 1H-1H NOESY

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	70 mM
4	H2O	natural abundance	93 %
5	D2O	[U-100% 2H]	7 %

5 2D 1H-31P HSQC

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	70 mM
9	D2O	[U-100% 2H]	100 %

6 2D 1H-13C HMBC (H1-H8 long range correlation)

Instrument

Varian VNMRS 500 - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(TPGPGPGPTPTPTPGPGPGPTPTPGPGPGPTPTPTPGPGP*G)-3')	natural abundance	5.0 ~ 6.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	70 mM
4	H2O	natural abundance	93 %
5	D2O	[U-100% 2H]	7 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19572_2mfu.nef
Input source #2: Coordindates	2mfu.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20-
TGGGTTTGGGTTGGGTTTGGG
|||||||||||||||||||||
TGGGTTTGGGTTGGGTTTGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0

Content subtype: combined_19572_2mfu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	162		100.0 (chain: A, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	608 (1)	noe	100.0 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 162

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DG	H21	9.87
3	DG	H22	7.06
4	DG	H21	9.98
4	DG	H22	6.39
8	DG	H22	6.53
9	DG	H21	9.32
9	DG	H22	7.12
10	DG	H22	6.77
13	DG	H22	5.47
14	DG	H21	9.09
14	DG	H22	6.88
15	DG	H21	8.25
19	DG	H21	10.43
19	DG	H22	6.03
20	DG	H22	6.81
21	DG	H22	6.34

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	146	73.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	105	71.4

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	41	80.4

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of restraints: 608
- Weight of restraints: 1.0 (608)
- Potential type of restraints: square-well-parabolic (608)
- Range of distance target values: 2.68, 7.23 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords G-Quadruplex

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 (0.314 seconds)

BMRB: 19572

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail