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Found 1 Document (0.425 seconds)

BMRB: 18626

2LWH

NMR Structure of the Self-Complementary 10 mer DNA Duplex 5'-GGATATATCC-3' in Complex with Netropsin

Authors

Rettig, M., Germann, M.W., Wilson, W., Wang, S.

Assembly

Self-Complementary 10 mer DNA Duplex 5'-GGATATATCC-3' in Complex with Netropsin

Entity

1. DNA 10 mer (polymer, Thiol state: not present), 10 monomers, 3106.988 × 2 Da Detail

GGATATATCC

2. NETROPSIN (non-polymer), 430.464 Da

Total weight

6644.44 Da

Max. entity weight

3106.988 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.5 %, Completeness (bb): 75.7 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	82.5 % (80 of 97)	82.5 % (80 of 97)
Suger, PO4	75.7 % (53 of 70)	75.7 % (53 of 70)
Nucleobase	100.0 % (27 of 27)	100.0 % (27 of 27)
Aromatic	100.0 % (20 of 20)	100.0 % (20 of 20)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA 10 mer

GGATATATCC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.9 mM
2	NETROPSIN	natural abundance	0.9 mM
3	D2O	natural abundance	100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
4	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.9 mM
5	NETROPSIN	natural abundance	0.9 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
8	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.6 mM
9	Pf1 phage	natural abundance	9 mg/mL
10	NETROPSIN	natural abundance	0.6 mM
11	D2O	natural abundance	100 %

Release date

2013-01-21

Citation

Molecular basis for sequence-dependent induced DNA bending
Rettig, M., Germann, M.W., Wang, S., Wilson, W.
Chembiochem. (2013), 14, 323-331, PubMed 23355266 , DOI 10.1002/cbic.201200706 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18625 released on 2013-01-21
Title NMR Structure of the Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'.

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz QXI probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.9 mM
2	NETROPSIN	natural abundance	0.9 mM
3	D2O	natural abundance	100 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz QXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
4	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.9 mM
5	NETROPSIN	natural abundance	0.9 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

3 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz QXI probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.9 mM
2	NETROPSIN	natural abundance	0.9 mM
3	D2O	natural abundance	100 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz TXI cryoprobe

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
8	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.6 mM
9	Pf1 phage	natural abundance	9 mg/mL
10	NETROPSIN	natural abundance	0.6 mM
11	D2O	natural abundance	100 %

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 500 MHz TXI cryoprobe

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
8	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.6 mM
9	Pf1 phage	natural abundance	9 mg/mL
10	NETROPSIN	natural abundance	0.6 mM
11	D2O	natural abundance	100 %

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 500 MHz TXI cryoprobe

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7

#	Name	Isotope labeling	Concentration
8	DNA (5'-D(GPGPAPTPAPTPAPTPCPC)-3')	natural abundance	0.6 mM
9	Pf1 phage	natural abundance	9 mg/mL
10	NETROPSIN	natural abundance	0.6 mM
11	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_18626_2lwh.nef
Input source #2: Coordindates	2lwh.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	NT	NETROPSIN	Assigned chemical shifts, Distance restraints, RDC restraints

Sequence alignments

Entity_assembly_ID (NMR): 1 vs Auth_asym_ID (model): 1
Entity_assembly_ID (NMR): 2 vs Auth_asym_ID (model): 2

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
1	1	10	0	0	100.0
2	2	10	0	0	100.0

Content subtype: combined_18626_2lwh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	182		100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10), 100.0 (chain: A, length: 1)
1	Distance restraints	AMBER_distance_constraints_2	Warning	592 (1)	noe	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10), 100.0 (chain: A, length: 1)
1	RDC restraints	AMBER_dipolar_coupling_3	Warning	39 (39)	.	90.0 (chain: 1, length: 10), 80.0 (chain: 2, length: 10), 100.0 (chain: A, length: 1)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: A, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 182
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DA	H61	7.43
3	DA	H62	6.02

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	79	81.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	52	74.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	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	8	8	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	DA	H61	7.42
13	DA	H62	6.01

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	80	82.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	53	75.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	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	8	8	100.0

Comp_index_ID	Comp_ID
1	NT

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: A, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 574
- Weight of restraints: 1.0 (574)
- Potential type of restraints: square-well-parabolic (574)
- Range of distance target values: 2.58, 5.89 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
  - Chain_ID: A
- Distance restraints on contact map

RDC restraints

Saveframe: AMBER_dipolar_coupling_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 90.0%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 80.0%
  - Entity_assembly_ID: A, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 39
- Potential type of restraints: square-well-parabolic (39)
- Range of observed RDC values: -2.5, 7.0 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: 1
    None
  - Chain_ID: 2
    None
  - Chain_ID: A
    None

Keywords ATATAT, DNA microstructure, DNA minor groove variations, Induced DNA binding, netropsin, NMR structure

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Found 1 Document (0.425 seconds)

BMRB: 18626

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail