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Found 1 Document (0.362 seconds)

BMRB: 18040

2LL9

DNA TT mismatch and 2,7-BisNP

Authors

JOURDAN, M., GRANZHAN, A., GUILLOT, R., DUMY, P., TEULADE-FICHOU, M.

Assembly

DNA 1

Entity

1. DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3') (polymer, Thiol state: not present), 11 monomers, 3428.168 Da Detail

CGTCGTAGTG C

2. DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3') (polymer, Thiol state: not present), 11 monomers, 3397.158 Da Detail

GCACTTCGAC G

Total weight

6825.326 Da

Max. entity weight

3428.168 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.7 %, Completeness (bb): 84.7 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	88.7 % (212 of 239)	88.5 % (192 of 217)	90.9 % (20 of 22)
Suger, PO4	84.7 % (149 of 176)	83.8 % (129 of 154)	90.9 % (20 of 22)
Nucleobase	100.0 % (63 of 63)	100.0 % (63 of 63)
Aromatic	100.0 % (44 of 44)	100.0 % (44 of 44)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3')

CGTCGTAGTG C

2. DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3')

GCACTTCGAC G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6

#	Name	Isotope labeling	Concentration
1	DNA_1	natural abundance	1.5 mM
2	DNA_2	natural abundance	1.5 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Release date

2012-03-01

Citation

Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch
Jourdan, M., Granzhan, A., Guillot, R., Dumy, P., Teulade-Fichou, M.
Nucleic Acids Res. (2012), 40, 5115-5128, PubMed 22362757 , DOI 10.1093/nar/gks067 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18050 released on 2012-03-01
Title Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18040_2ll9.nef
Input source #2: Coordindates	2ll9.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-
CGTCGTAGTGC
|||||||||||
CGTCGTAGTGC

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

-------20--
GCACTTCGACG
|||||||||||
GCACTTCGACG
--------10-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	11	0	0	100.0
B	B	11	0	0	100.0

Content subtype: combined_18040_2ll9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	212		100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)
1	Distance restraints	AMBER_distance_constraints_2	OK	232 (1)	noe	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)
1	Dihedral angle restraints	AMBER_dihedral_3	OK	218 (218)	.	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 192
  - ³¹P chemical shifts: 20
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	-4.62
3	DT	P	-4.84
4	DC	P	-4.84
5	DG	P	-4.51
6	DT	P	-5.03
7	DA	P	-4.61
8	DG	P	-4.51
9	DT	P	-4.84
10	DG	P	-4.82
11	DC	P	-4.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	97	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	66	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	DC	P	-5.03
14	DA	P	-4.5
15	DC	P	-4.82
16	DT	P	-4.96
17	DT	P	-5.14
18	DC	P	-3.72
19	DG	P	-3.72
20	DA	P	-4.87
21	DC	P	-4.84
22	DG	P	-4.51

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	95	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	63	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 232
- Weight of restraints: 1.0 (232)
- Potential type of restraints: square-well-parabolic (232)
- Range of distance target values: 1.88, 12.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 218
- Total number of restraints per polymer type: 218
- Weight of restraints: 1.0 (218)
- Potential type of restraints: square-well-parabolic (218)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA thymine mismatch

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Found 1 Document (0.362 seconds)

BMRB: 18040

Sample

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail