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BMRB: 25110

2MS9

Solution structure of a left-handed G-quadruplex

Authors

Chung, W., Heddi, B., Schmitt, E., Lim, K., Mechulam, Y., Phan, A.

Assembly

left-handed G-quadruplex

Entity

1. left-handed G-quadruplex (polymer, Thiol state: not present), 28 monomers, 8935.619 Da Detail

TGGTGGTGGT GGTTGTGGTG GTGGTGTT

Formula weight

8935.619 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.3 %, Completeness (bb): 90.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	88.3 % (233 of 264)	88.3 % (233 of 264)
Suger, PO4	90.3 % (177 of 196)	90.3 % (177 of 196)
Nucleobase	82.4 % (56 of 68)	82.4 % (56 of 68)
Aromatic	78.6 % (44 of 56)	78.6 % (44 of 56)
Methyl	100.0 % (12 of 12)	100.0 % (12 of 12)

1. DNA (28-MER)

TGGTGGTGGT GGTTGTGGTG GTGGTGTT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
2	DNA (28-MER)	[U-2% 15N]	0.2 ~ 0.5 mM
3	DNA (28-MER)	[U-100% 2H]	0.2 ~ 0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
7	DNA (28-MER)	[U-4% 13C; U-4% 15N]	0.2 ~ 1.0 mM
8	D2O	natural abundance	100 %

Release date

2015-10-15

Citation

Structure of a left-handed DNA G-quadruplex
Chung, W., Heddi, B., Schmitt, E., Lim, K., Mechulam, Y., Phan, A.
Proc. Natl. Acad. Sci. U. S. A. (2015), 112, 2729-2733, PubMed 25695967 , DOI 10.1073/pnas.1418718112 , Abstract

Experiments performed 8 experiments Detail

1 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
2	DNA (28-MER)	[U-2% 15N]	0.2 ~ 0.5 mM
3	DNA (28-MER)	[U-100% 2H]	0.2 ~ 0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
7	DNA (28-MER)	[U-4% 13C; U-4% 15N]	0.2 ~ 1.0 mM
8	D2O	natural abundance	100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
7	DNA (28-MER)	[U-4% 13C; U-4% 15N]	0.2 ~ 1.0 mM
8	D2O	natural abundance	100 %

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
7	DNA (28-MER)	[U-4% 13C; U-4% 15N]	0.2 ~ 1.0 mM
8	D2O	natural abundance	100 %

5 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
7	DNA (28-MER)	[U-4% 13C; U-4% 15N]	0.2 ~ 1.0 mM
8	D2O	natural abundance	100 %

6 2D 1H-13C JR HMBC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
2	DNA (28-MER)	[U-2% 15N]	0.2 ~ 0.5 mM
3	DNA (28-MER)	[U-100% 2H]	0.2 ~ 0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 15N-FILTERED

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
2	DNA (28-MER)	[U-2% 15N]	0.2 ~ 0.5 mM
3	DNA (28-MER)	[U-100% 2H]	0.2 ~ 0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 D-LABELED

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	0.2 ~ 2.0 mM
2	DNA (28-MER)	[U-2% 15N]	0.2 ~ 0.5 mM
3	DNA (28-MER)	[U-100% 2H]	0.2 ~ 0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25110_2ms9.nef
Input source #2: Coordindates	2ms9.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--------
TGGTGGTGGTGGTTGTGGTGGTGGTGTT
||||||||||||||||||||||||||||
TGGTGGTGGTGGTTGTGGTGGTGGTGTT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_25110_2ms9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	267		100.0 (chain: A, length: 28)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	714 (1)	noe	100.0 (chain: A, length: 28)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	64 (1)	hbond	57.1 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 267
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	DG	H21	9.189
5	DG	H22	4.338
8	DG	H21	9.433
8	DG	H22	4.548
17	DG	H21	9.333
17	DG	H22	4.426
20	DG	H21	9.346
20	DG	H22	4.758
23	DG	H21	4.644
23	DG	H22	9.495

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	264	233	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	177	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	56	82.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of restraints: 711
- Weight of restraints: 1.0 (711)
- Potential type of restraints: square-well-parabolic (711)
- Range of distance target values: 2.9, 6.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 57.1%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 1.95, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords G-quadruplex, Z-G4, left-handed helix

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Found 1 Document (0.364 seconds)

BMRB: 25110

Sample #1

Sample #2

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail