BMRBj - BMREntryMaster

Found 1 Document (0.773 seconds)

BMRB: 19280

2M92

Structure of d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid

Authors

Lim, K., Phan, A.

Assembly

d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid

Entity

1. d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid (polymer), 34 monomers, 10765.81 Da Detail

AGGGTGGGTG CTGGGGCGCG AAGCATTCGC GAGG

Formula weight

10765.81 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.3 %, Completeness (bb): 73.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	78.3 % (253 of 323)	78.3 % (253 of 323)
Suger, PO4	73.9 % (176 of 238)	73.9 % (176 of 238)
Nucleobase	90.6 % (77 of 85)	90.6 % (77 of 85)
Aromatic	94.1 % (64 of 68)	94.1 % (64 of 68)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. DNA (34-MER)

AGGGTGGGTG CTGGGGCGCG AAGCATTCGC GAGG

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 (34-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 (34-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 (34-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 (34-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 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 (34-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 (34-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 (34-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 (34-MER)	natural abundance		0.5-2.0 mM

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 (34-MER)	natural abundance		0.5-2.0 mM

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 (34-MER)	natural abundance		0.5-2.0 mM

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

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 (34-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 (34-MER)	[U-2% 15N]		0.5-2.0 mM

10 15N-FILTERED

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	Type	Concentration
5	DNA (34-MER)	[U-2% 15N]		0.5-2.0 mM

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
6	DNA (34-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_19280_2m92.nef
Input source #2: Coordindates	2m92.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----
AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG
||||||||||||||||||||||||||||||||||
AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_19280_2m92.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	263		100.0 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	958 (1)	noe	100.0 (chain: A, length: 34)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	2 (1)	noe	5.9 (chain: A, length: 34)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	88 (1)	hbond	82.4 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	64 (64)	.	73.5 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 263
- 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	323	253	78.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	238	176	73.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	77	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	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: 34, Sequence coverage: 100.0%
- Total number of restraints: 958
- Weight of restraints: 1.0 (958)
- Potential type of restraints: square-well-parabolic (958)
- Range of distance target values: 2.4, 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_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 5.9%
  - 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: 34, Sequence coverage: 82.4%
    - Total number of restraints: 88
    - Weight of restraints: 1.0 (88)
    - Potential type of restraints: square-well-parabolic (88)
    - 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: 34, Sequence coverage: 73.5%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA, duplex, duplex-quadruplex hybrid, quadruplex

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Found 1 Document (0.773 seconds)

BMRB: 19280

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Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail