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Found 1 Document (0.426 seconds)

BMRB: 19158

2M6V

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

Authors

Karsisiotis, A., Webba da Silva, M.

Assembly

DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')

Entity

1. DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3') (polymer, Thiol state: not present), 19 monomers, 6097.833 Da Detail

GGGTTGGGTT TTGGGTGGG

Formula weight

6097.833 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 78.2 %, Completeness (bb): 75.7 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	78.2 % (154 of 197)	86.5 % (154 of 178)	0.0 % (0 of 19)
Suger, PO4	75.7 % (115 of 152)	86.5 % (115 of 133)	0.0 % (0 of 19)
Nucleobase	86.7 % (39 of 45)	86.7 % (39 of 45)
Aromatic	84.2 % (32 of 38)	84.2 % (32 of 38)
Methyl	100.0 % (7 of 7)	100.0 % (7 of 7)

1. DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')

GGGTTGGGTT TTGGGTGGG

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPTPTPGPGPGPTPTPTPTPGPGPGPTPGPGP*G)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPTPTPGPGPGPTPTPTPTPGPGPGPTPGPGP*G)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 82.7 %, Completeness (bb): 85.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	82.7 % (326 of 394)	86.5 % (308 of 356)	47.4 % (18 of 38)
Suger, PO4	85.9 % (261 of 304)	91.4 % (243 of 266)	47.4 % (18 of 38)
Nucleobase	72.2 % (65 of 90)	72.2 % (65 of 90)
Aromatic	67.1 % (51 of 76)	67.1 % (51 of 76)
Methyl	100.0 % (14 of 14)	100.0 % (14 of 14)

1. DNA (5'-D(*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*G)-3')

GGGTTGGGTT TTGGGTGGG

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPGPTPTPGPGPGPTPTPTPTPGPGPGPTPGPGP*G)-3')	natural abundance		4.0 ~ 6.0 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(GPGPGPTPTPGPGPGPTPTPTPTPGPGPGPTPGPGP*G)-3')	natural abundance		4.0 ~ 6.0 mM
4	sodium phosphate	natural abundance		20 mM

Release date

2014-04-15

Citation

DNA quadruplex folding formalism--a tutorial on quadruplex topologies
Karsisiotis, A., Webba da Silva, C.
Methods (2013), 64, 28-35, PubMed 23791747 , DOI 10.1016/j.ymeth.2013.06.004 , Abstract

Experiments performed 6 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19158_2m6v.nef
Input source #2: Coordindates	2m6v.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---------
GGGTTGGGTTTTGGGTGGG
|||||||||||||||||||
GGGTTGGGTTTTGGGTGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_19158_2m6v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_non_exchangeable_protons_293K	Warning	167		100.0 (chain: A, length: 19)
2	Assigned chemical shifts	assigned_chem_shift_list_exchangeable_protons_278K	Warning	172		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	195 (1)	noe	84.2 (chain: A, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	347 (1)	noe	100.0 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_non_exchangeable_protons_293K
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 167
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	10.859
1	DG	H22	6.381
6	DG	H21	9.785
6	DG	H22	6.271
7	DG	H21	9.791
7	DG	H22	6.811
8	DG	H21	9.614
13	DG	H21	9.72
13	DG	H22	7.375
14	DG	H21	9.297
14	DG	H22	6.87
17	DG	H21	9.615
17	DG	H22	7.065

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	115	86.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	39	86.7

Saveframe: assigned_chem_shift_list_exchangeable_protons_278K

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 154
- ³¹P chemical shifts: 18

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	-4.45
3	DG	P	-3.952
4	DT	P	-3.47
5	DT	P	-4.243
6	DG	P	-4.871
7	DG	P	-4.732
8	DG	P	-4.232
9	DT	P	-3.895
10	DT	P	-4.089
11	DT	P	-4.562
12	DT	P	-3.192
13	DG	P	-4.079
14	DG	P	-4.394
15	DG	P	-5.657
16	DT	P	-5.623
17	DG	P	-4.915
18	DG	P	-4.383
19	DG	P	-4.463

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	178	154	86.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	128	96.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	26	57.8

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 84.2%
- Total number of restraints: 195
- Weight of restraints: 1.0 (195)
- Potential type of restraints: square-well-parabolic (195)
- Range of distance target values: 3.0, 5.0 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
  - Total number of restraints: 347
  - Weight of restraints: 1.0 (347)
  - Potential type of restraints: square-well-parabolic (347)
  - Range of distance target values: 2.27, 6.91 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords Folding Topology, G-Quadruplex

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Found 1 Document (0.426 seconds)

BMRB: 19158

Sample #1

Sample #2

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

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NMR combined restraints 5 contents Detail