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BMRB: 34162

5OGA

Structure of minimal i-motif domain

Authors

Mir, B., Serrano, I., Buitrago, D., Orozco, M., Escaja, N., Gonzalez, C.

Assembly

DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3')

Entity

1. DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3') (polymer, Thiol state: not present), 21 monomers, 6338.085 Da Detail

XXGTTCXGTT TTTCGTTCCG T

Formula weight

6338.085 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 76.2 %, Completeness: 40.0 %, Completeness (bb): 27.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	40.0 % (72 of 180)	40.0 % (72 of 180)
Suger, PO4	27.0 % (34 of 126)	27.0 % (34 of 126)
Nucleobase	70.4 % (38 of 54)	70.4 % (38 of 54)
Aromatic	63.9 % (23 of 36)	63.9 % (23 of 36)
Methyl	70.0 % (7 of 10)	70.0 % (7 of 10)

1. entity 1

XXGTTCXGTT TTTCGTTCCG T

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 0.5 mM LL3, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LL3	natural abundance		0.5 mM
2	NaPi	natural abundance		10 mM

Release date

2017-11-21

Citation

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH
Mir, B., Serrano, I., Buitrago, D., Orozco, M., Escaja, N., Gonzalez, C.
J. Am. Chem. Soc. (2017), 139, 13985-13988, PubMed 28933543 , DOI 10.1021/jacs.7b07383 , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34162_5oga.nef
Input source #2: Coordindates	5oga.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)
1:1:THM:O3'	1:2:DNR:P	unknown	unknown	n/a
1:2:DNR:O3'	1:3:DG:P	unknown	unknown	n/a
1:6:DC:O3'	1:7:DNR:P	unknown	unknown	n/a
1:7:DNR:O3'	1:8:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	THM	THYMIDINE	Assigned chemical shifts, Distance restraints, Coordinates
A	2	DNR	2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates
A	7	DNR	2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--------20-
XXGTTCXGTTTTTCGTTCCGT
|||||||||||||||||||||
XXGTTCXGTTTTTCGTTCCGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0

Content subtype: combined_34162_5oga.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	100		90.5 (chain: A, length: 21)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	104 (1)	noe	76.2 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 90.5%
- Total number of assignments
  - ¹H chemical shifts: 100
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
1	THM
2	DNR
7	DNR

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DG	H21	5.84
3	DG	H22	8.6
8	DG	H21	7.63
8	DG	H22	8.2
15	DG	H21	5.3
15	DG	H22	9.07
20	DG	H21	7.67
20	DG	H22	7.96

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	72	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	34	27.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	38	70.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	7	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	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: 21, Sequence coverage: 76.2%
- Total number of restraints: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: upper-bound-parabolic (104)
- Range of distance target values: 3.0, 6.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords DNA, DNA non-canonical structure, i-motif, minor groove tetrad

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Found 1 Document (0.41 seconds)

BMRB: 34162

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail