BMRBj - BMREntryMaster

Found 1 Document (0.406 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.406 seconds)

BMRB: 25840

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail