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Found 1 Document (0.463 seconds)

BMRB: 25840

2N89

Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH

Authors

Abou-Assi, R., Harkness, R.W., Martin-Pintado, N.W., Wilds, C.J., Campos-Olivas, R., Mittermaier, A.K., Gonzalez, C.W., Damha, M.J.

Assembly

Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC

Entity

1. Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC (polymer, Thiol state: not present), 6 monomers, 1804.099 × 4 Da Detail

TCCXXC

Total weight

7216.396 Da

Max. entity weight

1804.099 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 66.7 %, Completeness: 79.1 %, Completeness (bb): 67.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	79.1 % (34 of 43)	79.1 % (34 of 43)
Suger, PO4	67.9 % (19 of 28)	67.9 % (19 of 28)
Nucleobase	100.0 % (15 of 15)	100.0 % (15 of 15)
Aromatic	100.0 % (8 of 8)	100.0 % (8 of 8)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')

TCCXXC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPCPCP(CFL)P(CFL)PC)-3')	natural abundance		1.25 mM
2	sodium chloride	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
3	DNA (5'-D(TPCPCP(CFL)P(CFL)PC)-3')	natural abundance		1.25 mM
4	sodium chloride	natural abundance		10 mM

Release date

2016-08-14

Citation

Stabilization of i-motif structures by 2'-β-fluorination of DNA
Abou-Assi, H., Harkness, R.W., Martin-Pintado, N., Wilds, C.J., Campos-Olivas, R., Mittermaier, A.K., Gonzalez, C., Damha, M.J.
Nucleic Acids Res. (2016), 44, 4998-5009, PubMed 27166371 , DOI 10.1093/nar/gkw402 , Abstract

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25840_2n89.nef
Input source #2: Coordindates	2n89.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)
1:3:DC:O3'	1:4:CFL:P	unknown	unknown	n/a
1:4:CFL:O3'	1:5:CFL:P	unknown	unknown	n/a
1:5:CFL:O3'	1:6:DC:P	unknown	unknown	n/a
2:3:DC:O3'	2:4:CFL:P	unknown	unknown	n/a
2:4:CFL:O3'	2:5:CFL:P	unknown	unknown	n/a
2:5:CFL:O3'	2:6:DC:P	unknown	unknown	n/a
3:3:DC:O3'	3:4:CFL:P	unknown	unknown	n/a
3:4:CFL:O3'	3:5:CFL:P	unknown	unknown	n/a
3:5:CFL:O3'	3:6:DC:P	unknown	unknown	n/a
4:3:DC:O3'	4:4:CFL:P	unknown	unknown	n/a
4:4:CFL:O3'	4:5:CFL:P	unknown	unknown	n/a
4:5:CFL:O3'	4:6:DC:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	4	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
A	5	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
B	10	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
B	11	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
C	16	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
C	17	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
D	22	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
D	23	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates

Sequence alignments

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

------
TCCXXC
||||||
TCCXXC

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

--10--
TCCXXC
||||||
TCCXXC
------

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

------
TCCXXC
||||||
TCCXXC

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

-20---
TCCXXC
||||||
TCCXXC
------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	6	100.0
B	B	6	100.0
C	C	6	100.0
D	D	6	100.0

Content subtype: combined_25840_2n89.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	49		100.0 (chain: A, length: 6)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	140 (1)	noe	100.0 (chain: A, length: 6), 100.0 (chain: B, length: 6), 100.0 (chain: C, length: 6), 100.0 (chain: D, length: 6)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
4	CFL
5	CFL

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	35	81.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	20	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	1	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: 6, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 6, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 6, Sequence coverage: 100.0%
- Total number of restraints: 140
- Weight of restraints: 1.0 (140)
- Potential type of restraints: upper-bound-parabolic (140)
- Range of distance target values: 2.0, 4.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map

Keywords 2'F-ANA, 2'F-araC, Modified nucleotides, i-motif

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Found 1 Document (0.463 seconds)

BMRB: 25840

Sample #1

Sample #2

Experiments performed 5 experiments Detail

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Sample

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NMR combined restraints 3 contents Detail