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Found 1 Document (0.457 seconds)

BMRB: 19281

2M93

Structure of d[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] duplex-quadruplex hybrid

Authors

Lim, K., Phan, A.

Assembly

d[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] duplex-quadruplex hybrid

Entity

1. d[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] duplex-quadruplex hybrid (polymer, Thiol state: not present), 32 monomers, 10129.39 Da Detail

TTGGGTGGGC GCGAAGCATT CGCGGGGTGG GT

Formula weight

10129.39 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.7 %, Completeness (bb): 78.6 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	80.7 % (246 of 305)	80.7 % (246 of 305)
Suger, PO4	78.6 % (176 of 224)	78.6 % (176 of 224)
Nucleobase	86.4 % (70 of 81)	86.4 % (70 of 81)
Aromatic	89.1 % (57 of 64)	89.1 % (57 of 64)
Methyl	100.0 % (7 of 7)	100.0 % (7 of 7)

1. DNA (32-MER)

TTGGGTGGGC GCGAAGCATT CGCGGGGTGG GT

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 (32-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 (32-MER)	natural abundance		0.5-2.0 mM

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
5	DNA (32-MER)	[U-2% 15N]		0.5-2.0 mM

Sample #4

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

#	Name	Isotope labeling	Type	Concentration
6	DNA (32-MER)	[U-100% 2H]		0.5-2.0 mM

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 10 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 (32-MER)	natural abundance		0.5-2.0 mM

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 (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

3 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 (32-MER)	natural abundance		0.5-2.0 mM

4 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 (32-MER)	natural abundance		0.5-2.0 mM

5 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 (32-MER)	natural abundance		0.5-2.0 mM

6 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 (32-MER)	natural abundance	0.5-2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 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 (32-MER)	natural abundance		0.5-2.0 mM

8 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 (32-MER)	natural abundance		0.5-2.0 mM

9 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	Type	Concentration
5	DNA (32-MER)	[U-2% 15N]		0.5-2.0 mM

10 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
6	DNA (32-MER)	[U-100% 2H]		0.5-2.0 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19281_2m93.nef
Input source #2: Coordindates	2m93.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--------30--
TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT
||||||||||||||||||||||||||||||||
TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0

Content subtype: combined_19281_2m93.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	260		100.0 (chain: A, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1088 (1)	noe	100.0 (chain: A, length: 32)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	5 (1)	noe	18.8 (chain: A, length: 32)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	74 (1)	hbond	68.8 (chain: A, length: 32)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	74 (74)	.	75.0 (chain: A, length: 32)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 260
- 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	305	246	80.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	224	176	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	81	70	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	23	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: 32, Sequence coverage: 100.0%
- Total number of restraints: 1087
- Weight of restraints: 1.0 (1087)
- Potential type of restraints: square-well-parabolic (1087)
- Range of distance target values: 2.4, 6.5 (Å)
- Histogram of 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: 32, Sequence coverage: 18.8%
  - Total number of restraints: 5
  - Weight of restraints: 1.0 (5)
  - Potential type of restraints: square-well-parabolic (5)
  - 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: 32, Sequence coverage: 68.8%
    - Total number of restraints: 74
    - Weight of restraints: 1.0 (74)
    - Potential type of restraints: square-well-parabolic (74)
    - 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: 32, Sequence coverage: 75.0%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA, duplex, duplex-quadruplex hybrid, quadruplex

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Found 1 Document (0.457 seconds)

BMRB: 19281

Sample #1

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Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail