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Found 1 Document (0.432 seconds)

BMRB: 18625

2LWG

NMR Structure of the Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'.

Authors

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

Assembly

Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'

Entity

1. Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3' (polymer, Thiol state: not present), 10 monomers, 3106.988 × 2 Da Detail

GGATATATCC

Total weight

6213.976 Da

Max. entity weight

3106.988 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.7 %, Completeness (bb): 87.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	90.7 % (88 of 97)	90.7 % (88 of 97)
Suger, PO4	87.1 % (61 of 70)	87.1 % (61 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 (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')

GGATATATCC

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	GGATATATCC	natural abundance		0.9 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
2	GGATATATCC	natural abundance		0.9 mM

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
3	GGATATATCC	natural abundance		1.2 mM
4	Pf1 phage	natural abundance		11 mg/mL

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: 18626 released on 2013-01-21
Title NMR Structure of the Self-Complementary 10 mer DNA Duplex 5'-GGATATATCC-3' in Complex with Netropsin

Experiments performed 6 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_18625_2lwg.nef
Input source #2: Coordindates	2lwg.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): 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_18625_2lwg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	94		100.0 (chain: 1, length: 10)
1	Distance restraints	AMBER_distance_constraints_2	Warning	626 (1)	noe	100.0 (chain: 1, length: 10), 100.0 (chain: 2, length: 10)
1	RDC restraints	AMBER_dipolar_coupling_3	OK	46 (46)	.	90.0 (chain: 1, length: 10), 90.0 (chain: 2, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 94
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DA	H61	7.598
3	DA	H62	6.028
5	DA	H61	7.442
5	DA	H62	6.215
7	DA	H61	7.477
7	DA	H62	6.23

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	88	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	61	87.1

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

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%
- Total number of restraints: 624
- Weight of restraints: 1.0 (624)
- Potential type of restraints: square-well-parabolic (624)
- Range of distance target values: 2.55, 6.13 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
- Distance restraints on contact map

RDC restraints

Saveframe: AMBER_dipolar_coupling_3
- Status: OK
- 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: 90.0%
- Total number of restraints: 46
- Potential type of restraints: square-well-parabolic (46)
- Range of observed RDC values: -1.5, 18.3 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: 1
    None
  - Chain_ID: 2
    None

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

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Found 1 Document (0.432 seconds)

BMRB: 18625

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 6 experiments Detail

Instrument

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Sample

Instrument

Sample

Instrument

Sample

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Sample

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NMR combined restraints 4 contents Detail