BMRBj - BMREntryMaster

Found 1 Document (0.405 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.405 seconds)

BMRB: 19280

Sample #1

Sample #2

Sample #3

Sample #4

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail