BMRBj - BMREntryMaster

Found 1 Document (0.448 seconds)

BMRB: 18452

2LSX

Solution structure of a mini i-motif

Authors

Escaja, N., Viladoms, J., Villasante, A., Pedroso, E., Gonzalez, C.

Assembly

Synthetic cyclic oligonucleotide

Entity

1. Synthetic cyclic oligonucleotide (polymer, Thiol state: not present), 10 monomers, 3079.946 Da Detail

TCGTTTCGTT

2. DNA 1 (polymer, Thiol state: not present), 10 monomers, 3079.946 Da Detail

TCGTTTCGTT

3. Synthetic cyclic oligonucleotide, entity 3 (polymer), 10 monomers, 945.0265 × 2 Da Detail

TCGTTTCGTT

Total weight

8049.9453 Da

Max. entity weight

3079.946 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 33.3 %, Completeness: 42.0 %, Completeness (bb): 43.2 % Detail

Polymer type: polydeoxyribonucleotide polypeptide(L)

	Total	¹H
All	42.0 % (100 of 238)	42.0 % (100 of 238)
Backbone	43.2 % (70 of 162)	43.2 % (70 of 162)
Sidechain	39.5 % (30 of 76)	39.5 % (30 of 76)
Aromatic	50.0 % (20 of 40)	50.0 % (20 of 40)
Methyl	33.3 % (6 of 18)	33.3 % (6 of 18)

1. Synthetic cyclic oligonucleotide

TCGTTTCGTT

2. DNA 1

TCGTTTCGTT

3. entity 3

TCGTTTCGTT

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 279 K, pH 5.0, Details 120 mM NACl; 90% H2O, 10% D2O pH 5.0

#	Name	Isotope labeling	Concentration
1	Synthetic cyclic oligonucleotide	natural abundance	0.5 mM
2	NaCl	natural abundance	150 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Release date

2012-10-14

Citation

A minimal i-motif stabilized by minor groove G:T:G:T tetrads
Escaja, N., Viladoms, J., Garavis, M., Villasante, A., Pedroso, E., Gonzalez, C.
Nucleic Acids Res. (2012), 40, 11737-11747, PubMed 23042679 , DOI 10.1093/nar/gks911 , Abstract

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18452_2lsx.nef
Input source #2: Coordindates	2lsx.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:10:DT:O3'	1:1:DT:P	unknown	unknown	n/a
2:10:DT:O3'	2:1:DT:P	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10
TCGTTTCGTT
||||||||||
TCGTTTCGTT

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

--------10
TCGTTTCGTT
||||||||||
TCGTTTCGTT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	10	0	0	100.0
B	B	10	0	0	100.0

Content subtype: combined_18452_2lsx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	104		100.0 (chain: A, length: 10)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	267 (1)	noe	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DG	H21	5.69
3	DG	H22	8.83
8	DG	H21	5.69
8	DG	H22	8.83

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	100	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0

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	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 267
- Weight of restraints: 1.0 (267)
- Potential type of restraints: upper-bound-parabolic (267)
- Range of distance target values: 2.0, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords cylic oligonucleotide, hemiprotonated base pair, minor groove tetrad, quadruplex

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Found 1 Document (0.448 seconds)

BMRB: 18452

Sample

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail