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BMRB: 17980

2LK7

Monomer-dimer equilibrium for 5 -5 stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study

Authors

Do, N., Phan, A.

Assembly

G-quadruplexes

Entity

1. G-quadruplexes (polymer, Thiol state: not present), 18 monomers, 5793.640 Da Detail

TTGGGTGGGT GGGTGGGT

Formula weight

5793.64 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.5 %, Completeness (bb): 97.6 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	87.5 % (147 of 168)	87.5 % (147 of 168)
Suger, PO4	97.6 % (123 of 126)	97.6 % (123 of 126)
Nucleobase	57.1 % (24 of 42)	57.1 % (24 of 42)
Aromatic	50.0 % (18 of 36)	50.0 % (18 of 36)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')

TTGGGTGGGT GGGTGGGT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	G-quadruplexes	natural abundance	0.5 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Release date

2012-10-08

Citation

Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study
Do, N., Phan, A.
Chemistry (2012), 18, 14752-14759, PubMed 23019076 , DOI 10.1002/chem.201103295 , Abstract

Related entities 1. G-quadruplexes, : 2 entities Detail

Experiments performed 1 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17980_2lk7.nef
Input source #2: Coordindates	2lk7.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--------
TTGGGTGGGTGGGTGGGT
||||||||||||||||||
TTGGGTGGGTGGGTGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0

Content subtype: combined_17980_2lk7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	159		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	410 (1)	noe	100.0 (chain: A, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	15 (1)	noe	66.7 (chain: A, length: 18)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	48 (1)	hbond	66.7 (chain: A, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	29 (29)	.	100.0 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 159
- 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	168	147	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	123	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	24	57.1

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	12	12	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 410
- Weight of restraints: 1.0 (410)
- Potential type of restraints: square-well-parabolic (410)
- Range of distance target values: 2.0, 7.5 (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: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 66.7%
  - Total number of restraints: 15
  - Weight of restraints: 1.0 (15)
  - Potential type of restraints: square-well-parabolic (15)
  - Range of distance target values: 42.25, 42.25 (Å)
  - 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: 18, Sequence coverage: 66.7%
    - Total number of restraints: 48
    - Weight of restraints: 1.0 (48)
    - Potential type of restraints: square-well-parabolic (48)
    - Range of distance target values: 1.99, 2.95 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 29
- Total number of restraints per polymer type: 29
- Weight of restraints: 1.0 (29)
- Potential type of restraints: square-well-parabolic (29)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords G-quadruplex, NMR, equilibrium, stacking

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Found 1 Document (0.38 seconds)

BMRB: 17980

Sample

Related entities 1. G-quadruplexes, : 2 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 6 contents Detail