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Found 1 Document (0.416 seconds)

BMRB: 19389

2MB4

Solution structure of a stacked dimeric G-quadruplex formed by a segment of the human CEB1 minisatellite

Authors

Adrian, M., Ang, D., Lech, C., Heddi, B., Nicolas, A., Phan, A.

Assembly

stacked dimeric G-quadruplex

Entity

1. stacked dimeric G-quadruplex (polymer, Thiol state: not present), 18 monomers, 5870.708 × 2 Da Detail

AGGGGGGAGG GAGGGTGG

Total weight

11741.416 Da

Max. entity weight

5870.708 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.0 %, Completeness (bb): 77.8 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	81.0 % (132 of 163)	81.0 % (132 of 163)
Suger, PO4	77.8 % (98 of 126)	77.8 % (98 of 126)
Nucleobase	91.9 % (34 of 37)	91.9 % (34 of 37)
Aromatic	91.7 % (33 of 36)	91.7 % (33 of 36)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*TP*GP*G)-3')

AGGGGGGAGG GAGGGTGG

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 (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
2	potassium phosphate	natural abundance	20 mM
3	potassium chloride	natural abundance	70 mM
4	DSS	natural abundance	10 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

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

#	Name	Isotope labeling	Concentration
7	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
8	potassium phosphate	natural abundance	20 mM
9	potassium chloride	natural abundance	70 mM
10	DSS	natural abundance	10 uM
11	D2O	natural abundance	100 %

Release date

2014-05-26

Citation

Structure and conformational dynamics of a stacked dimeric G-quadruplex formed by the human CEB1 minisatellite
Adrian, M., Ang, D., Lech, C.J., Heddi, B., Nicolas, A., Phan, A.
J. Am. Chem. Soc. (2014), 136, 6297-6305, PubMed 24742225 , DOI 10.1021/ja4125274 , Abstract

Experiments performed 5 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
2	potassium phosphate	natural abundance	20 mM
3	potassium chloride	natural abundance	70 mM
4	DSS	natural abundance	10 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
7	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
8	potassium phosphate	natural abundance	20 mM
9	potassium chloride	natural abundance	70 mM
10	DSS	natural abundance	10 uM
11	D2O	natural abundance	100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
7	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
8	potassium phosphate	natural abundance	20 mM
9	potassium chloride	natural abundance	70 mM
10	DSS	natural abundance	10 uM
11	D2O	natural abundance	100 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
2	potassium phosphate	natural abundance	20 mM
3	potassium chloride	natural abundance	70 mM
4	DSS	natural abundance	10 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 2D 1H-1H ROESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(APGPGPGPGPGPGPAPGPGPGPAPGPGPGPTPGPG)-3')	natural abundance	1.5 mM
2	potassium phosphate	natural abundance	20 mM
3	potassium chloride	natural abundance	70 mM
4	DSS	natural abundance	10 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19389_2mb4.nef
Input source #2: Coordindates	2mb4.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--------
AGGGGGGAGGGAGGGTGG
||||||||||||||||||
AGGGGGGAGGGAGGGTGG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------
AGGGGGGAGGGAGGGTGG
||||||||||||||||||
AGGGGGGAGGGAGGGTGG

Chain assignments

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

Content subtype: combined_19389_2mb4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	134		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1102 (1)	noe	100.0 (chain: B, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	96 (1)	hbond	66.7 (chain: B, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	62 (62)	.	66.7 (chain: B, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 134
- 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	163	132	81.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	98	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	34	91.9

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 1102
- Weight of restraints: 1.0 (1102)
- Potential type of restraints: square-well-parabolic (1102)
- 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
    None
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 66.7%
  - Total number of restraints: 96
  - Weight of restraints: 1.0 (96)
  - Potential type of restraints: square-well-parabolic (96)
  - Range of distance target values: 1.95, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
  - 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: B, Chain length: 18, Sequence coverage: 66.7%
- Total number of restraints: 62
- Total number of restraints per polymer type: 62
- Weight of restraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (62)
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords CEB1, G-quadruplex, minisatellite, Stacking

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Found 1 Document (0.416 seconds)

BMRB: 19389

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail