BMRBj - BMREntryMaster

Found 1 Document (0.398 seconds)

BMRB: 19277

2M8Z

Structure of d[GGTTGGCGCGAAGCATTCGCGGGTTGG] duplex-quadruplex hybrid

Authors

Lim, K., Phan, A.

Assembly

d[GGTTGGCGCGAAGCATTCGCGGGTTGG] duplex-quadruplex hybrid

Entity

1. d[GGTTGGCGCGAAGCATTCGCGGGTTGG] duplex-quadruplex hybrid (polymer, Thiol state: not present), 27 monomers, 8508.375 Da Detail

GGTTGGCGCG AAGCATTCGC GGGTTGG

Formula weight

8508.375 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.0 %, Completeness (bb): 86.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	88.0 % (228 of 259)	88.0 % (228 of 259)
Suger, PO4	86.2 % (163 of 189)	86.2 % (163 of 189)
Nucleobase	92.9 % (65 of 70)	92.9 % (65 of 70)
Aromatic	94.4 % (51 of 54)	94.4 % (51 of 54)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. DNA (27-MER)

GGTTGGCGCG AAGCATTCGC GGGTTGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (27-MER)	[U-2% 15N]	0.5-2.0 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	DNA (27-MER)	[U-100% 2H]		0.5-2.0 mM
10	D2O	natural abundance		100 %

Release date

2013-07-07

Citation

Structural basis of DNA quadruplex-duplex junction formation
Lim, K., Phan, A.
Angew. Chem Int Ed Engl. (2013), 52, 8566-8569, PubMed 23794476 , DOI 10.1002/anie.201302995 , Abstract

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

2 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

3 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 2D 1H-1H COSY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

7 2D 1H-13C JR HMBC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 2D 1H-31P HSQC

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

9 H-D EXCHANGE

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		0.5-2.0 mM
5	D2O	natural abundance		100 %

10 15N-FILTERED

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (27-MER)	[U-2% 15N]	0.5-2.0 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 D-LABELED

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	DNA (27-MER)	[U-100% 2H]		0.5-2.0 mM
10	D2O	natural abundance		100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19277_2m8z.nef
Input source #2: Coordindates	2m8z.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-------
GGTTGGCGCGAAGCATTCGCGGGTTGG
|||||||||||||||||||||||||||
GGTTGGCGCGAAGCATTCGCGGGTTGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_19277_2m8z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	240		100.0 (chain: A, length: 27)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1170 (1)	noe	100.0 (chain: A, length: 27)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	2 (1)	noe	7.4 (chain: A, length: 27)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	64 (1)	hbond	74.1 (chain: A, length: 27)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	68 (68)	.	74.1 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 240
- 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	259	228	88.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	163	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	65	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of restraints: 1163
- Weight of restraints: 1.0 (1163)
- Potential type of restraints: square-well-parabolic (1163)
- Range of distance target values: 2.4, 6.5 (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_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 7.4%
  - Total number of restraints: 2
  - Weight of restraints: 1.0 (2)
  - Potential type of restraints: square-well-parabolic (2)
  - Range of distance target values: 42.1, 42.1 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 74.1%
    - Total number of restraints: 64
    - Weight of restraints: 1.0 (64)
    - Potential type of restraints: square-well-parabolic (64)
    - Range of distance target values: 2.0, 2.9 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 74.1%
- Total number of restraints: 68
- Total number of restraints per polymer type: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: square-well-parabolic (68)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA, duplex, duplex-quadruplex hybrid, quadruplex

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Found 1 Document (0.398 seconds)

BMRB: 19277

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Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail