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Found 1 Document (0.347 seconds)

BMRB: 17351

2L7D

Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2

Authors

DeRose, E.F., Perera, L., Michael, M.S., Thomas, K.A., Robert, L.E.

Assembly

rG4 substituted Drew Dickerson dodecamer

Entity

1. rG4 substituted Drew Dickerson dodecamer (polymer, Thiol state: not present), 12 monomers, 3742.364 × 2 Da Detail

CGCGAATTCG CG

Total weight

7484.728 Da

Max. entity weight

3742.364 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.2 %, Completeness (bb): 92.6 % Detail

Polymer type: DNA/RNA hybrid

	Total	¹H	³¹P
All	92.2 % (119 of 129)	92.3 % (108 of 117)	91.7 % (11 of 12)
Suger, PO4	92.6 % (88 of 95)	92.8 % (77 of 83)	91.7 % (11 of 12)
Nucleobase	91.2 % (31 of 34)	91.2 % (31 of 34)
Aromatic	95.8 % (23 of 24)	95.8 % (23 of 24)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. rG4 substituted Drew Dickerson dodecamer

CGCGAATTCG CG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
6	sodium chloride	natural abundance	50.0 mM
7	sodium phosphate	natural abundance	50.0 mM
8	EDTA	natural abundance	0.5 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
12	sodium chloride	natural abundance	50.0 mM
13	sodium phosphate	natural abundance	50.0 mM
14	EDTA	natural abundance	0.5 mM
15	D2O	natural abundance	100 %

Release date

2015-10-21

Citation

Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide
DeRose, E.F., Perera, L., Murray, M.S., Kunkel, T.A., London, R.E.
Biochemistry (2012), 51, 2407-2416, PubMed 22390730 , DOI 10.1021/bi201710q , Abstract

Related entities 1. rG4 substituted Drew Dickerson dodecamer, : 4 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

3 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

4 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
6	sodium chloride	natural abundance	50.0 mM
7	sodium phosphate	natural abundance	50.0 mM
8	EDTA	natural abundance	0.5 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
6	sodium chloride	natural abundance	50.0 mM
7	sodium phosphate	natural abundance	50.0 mM
8	EDTA	natural abundance	0.5 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 2D 1H-31P COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

7 2D 1H-31P J-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

8 2D 1H-31P HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

9 2D 1H-31P HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
6	sodium chloride	natural abundance	50.0 mM
7	sodium phosphate	natural abundance	50.0 mM
8	EDTA	natural abundance	0.5 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 2D CT-NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
2	sodium chloride	natural abundance	50.0 mM
3	sodium phosphate	natural abundance	50.0 mM
4	EDTA	natural abundance	0.5 mM

11 2D CT-NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	rG4 substituted Drew Dickerson dodecamer	natural abundance	2.0 mM
6	sodium chloride	natural abundance	50.0 mM
7	sodium phosphate	natural abundance	50.0 mM
8	EDTA	natural abundance	0.5 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17351_2l7d.nef
Input source #2: Coordindates	2l7d.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	Error

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--
CGCGAATTCGCG
||||||||||||
CGCGAATTCGCG

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

------20----
CGCGAATTCGCG
||||||||||||
CGCGAATTCGCG
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_17351_2l7d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	120		100.0 (chain: A, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Error	212 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	72 (1)	hbond	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	68 (68)	.	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	Error	158 (158)	.	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_7	Error	22 (22)	.	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 109
  - ³¹P chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	-4.1741
3	DC	P	-4.3245
4	G	HO2'	4.9799
4	G	P	-4.2852
5	DA	P	-2.6935
6	DA	P	-4.5003
7	DT	P	-4.552
8	DT	P	-4.5348
9	DC	P	-4.4044
10	DG	P	-3.8562
11	DC	P	-4.2421
12	DG	P	-4.0181

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	108	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	77	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	31	91.2

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	8	8	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 212
- Weight of restraints: 1.0 (212)
- Potential type of restraints: square-well-parabolic (212)
- Range of distance target values: 2.0, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Total number of restraints: 72
  - Weight of restraints: 1.0 (72)
  - Potential type of restraints: square-well-parabolic (72)
  - Range of distance target values: 1.81, 3.69 (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: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 68
- Total number of restraints per polymer type: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: square-well-parabolic (68)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: Error
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 158
- Potential type of restraints: square-well-parabolic (158)
- Range of observed RDC values: -10.9, 10.43 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None
- Saveframe: CNS/XPLOR_dipolar_coupling_7
  - Status: Error
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Total number of restraints: 22
  - Potential type of restraints: square-well-parabolic (22)
  - Range of observed RDC values: -0.12, 2.07 (Hz)
  - Histogram of observed RDC values
  - RDC restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
      None

Keywords B-DNA, A-DNA, Ribonucleotide substituted DNA

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Found 1 Document (0.347 seconds)

BMRB: 17351

Sample #1

Sample #2

Sample #3

Related entities 1. rG4 substituted Drew Dickerson dodecamer, : 4 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 7 contents Detail