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Found 1 Document (0.361 seconds)

BMRB: 30055

5J4P

DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium

Authors

Dvorkin, S.A., Webba da Silva, M.

Assembly

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

Entity

1. DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*TP*GP*GP*TP*TP*TP*GP*G)-3') (polymer, Thiol state: not present), 18 monomers, 5693.588 Da Detail

GGTTTGGTTT TGGTTTGG

Formula weight

5693.588 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.4 %, Completeness (bb): 91.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	92.4 % (159 of 172)	92.4 % (159 of 172)
Suger, PO4	91.3 % (115 of 126)	91.3 % (115 of 126)
Nucleobase	95.7 % (44 of 46)	95.7 % (44 of 46)
Aromatic	94.4 % (34 of 36)	94.4 % (34 of 36)
Methyl	100.0 % (10 of 10)	100.0 % (10 of 10)

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

GGTTTGGTTT TGGTTTGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278.15 K, pH 6.8, Details 2 mM no dna, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNA	none	2 (±0.5) mM
2	NaPi	natural abundance	100 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278.15 K, pH 6.8, Details 2 mM no dna, 100% D2O

#	Name	Isotope labeling	Concentration
5	DNA	none	2 (±0.5) mM
6	NaPi	natural abundance	100 mM
7	D2O	natural abundance	100 %

Release date

2016-04-03

Citation

Encoding canonical DNA quadruplex structure
Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.
Sci. Adv. (2018), 4, eaat3007-eaat3007, PubMed 30182059 , DOI 10.1126/sciadv.aat3007 , 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_30055_5j4p.nef
Input source #2: Coordindates	5j4p.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--------
GGTTTGGTTTTGGTTTGG
||||||||||||||||||
GGTTTGGTTTTGGTTTGG

Chain assignments

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

Content subtype: combined_30055_5j4p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	173		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	618 (1)	noe	100.0 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_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: 173
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H22	10.71
1	DG	H21	6.29
2	DG	H22	10.39
2	DG	H21	6.83
6	DG	H22	9.9
6	DG	H21	7.03
7	DG	H22	9.5
7	DG	H21	6.9
12	DG	H22	9.53
12	DG	H21	7.59
13	DG	H22	9.64
13	DG	H21	6.68
17	DG	H22	9.24
17	DG	H21	7.06

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	172	159	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	115	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	44	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 618
- Weight of restraints: 1.0 (618)
- Potential type of restraints: square-well-parabolic (618)
- Range of distance target values: 2.36, 5.0 (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, Structure from MOLMOL, Structure from programmed design

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Found 1 Document (0.361 seconds)

BMRB: 30055

Sample #1

Sample #2

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail