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Found 1 Document (0.382 seconds)

BMRB: 19571

2MFT

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

Authors

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

Assembly

d(GGGTTTTGGGTGGGTTTTGGG) quadruplex

Entity

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

GGGTTTTGGG TGGGTTTTGG G

Formula weight

6706.218 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 79.8 %, Completeness (bb): 87.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	79.8 % (158 of 198)	79.8 % (158 of 198)
Suger, PO4	87.1 % (128 of 147)	87.1 % (128 of 147)
Nucleobase	58.8 % (30 of 51)	58.8 % (30 of 51)
Aromatic	50.0 % (21 of 42)	50.0 % (21 of 42)
Methyl	100.0 % (9 of 9)	100.0 % (9 of 9)

1. DNA

GGGTTTTGGG TGGGTTTTGG G

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

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

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Concentration
5	DNA (5'-D(GPGPGPTPTPTPTPGPGPGPTPGPGPGPTPTPTPTPGPGP*G)-3')	natural abundance	2 mM
6	sodium phosphate	natural abundance	20 mM
7	D2O	[U-100% 2H]	100 %

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 74.5 %, Completeness (bb): 75.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	74.5 % (295 of 396)	74.5 % (295 of 396)
Suger, PO4	75.2 % (221 of 294)	75.2 % (221 of 294)
Nucleobase	72.5 % (74 of 102)	72.5 % (74 of 102)
Aromatic	66.7 % (56 of 84)	66.7 % (56 of 84)
Methyl	100.0 % (18 of 18)	100.0 % (18 of 18)

1. DNA

GGGTTTTGGG TGGGTTTTGG G

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

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

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.8

#	Name	Isotope labeling	Concentration
5	DNA (5'-D(GPGPGPTPTPTPTPGPGPGPTPGPGPGPTPTPTPTPGPGP*G)-3')	natural abundance	2 mM
6	sodium phosphate	natural abundance	20 mM
7	D2O	[U-100% 2H]	100 %

Release date

2013-10-31

Citation

Encoding canonical DNA quadruplex structure
Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.
Sci. Adv. (2018), 4, eaat3007-eaat3007, PubMed 30182059 , DOI 10.1126/sciadv.aat3007 , Abstract

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19571_2mft.nef
Input source #2: Coordindates	2mft.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-
GGGTTTTGGGTGGGTTTTGGG
|||||||||||||||||||||
GGGTTTTGGGTGGGTTTTGGG

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_19571_2mft.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	158		100.0 (chain: A, length: 21)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	151		100.0 (chain: A, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	688 (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: 158
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	158	79.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	128	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	30	58.8

Saveframe: assigned_chem_shift_list_2

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: 151

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H22	10.184
1	DG	H21	6.215
8	DG	H22	8.842
8	DG	H21	6.857
9	DG	H22	9.395
9	DG	H21	6.776
12	DG	H22	10.822
12	DG	H21	5.968
19	DG	H22	9.549
19	DG	H21	7.299
20	DG	H22	9.434
20	DG	H21	6.722
21	DG	H22	9.082
21	DG	H21	6.615

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	137	69.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	93	63.3

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	44	86.3

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: 688
- Weight of restraints: 1.0 (688)
- Potential type of restraints: square-well-parabolic (688)
- Range of distance target values: 2.02, 6.0 (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

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Found 1 Document (0.382 seconds)

BMRB: 19571

Sample #1

Sample #2

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

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Instrument

Sample

Instrument

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Instrument

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NMR combined restraints 4 contents Detail