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Found 1 Document (0.379 seconds)

BMRB: 11608

2RVP

SOLUTION STRUCTURE OF DNA CONTAINING METALLO-BASE-PAIR

Authors

Dairaku, T., Furuita, K., Sato, H., Sebera, J., Nakashima, K., Kondo, J., Yamanaka, D., Kondo, Y., Okamoto, I., Ono, A., Sychrovsky, V., Kojima, C., Tanaka, Y.

Assembly

DNA CONTAINING METALLO-BASE-PAIR

Entity

1. DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3') (polymer, Thiol state: not present), 15 monomers, 4628.993 Da Detail

TAATATACTT AATTA

2. DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3') (polymer, Thiol state: not present), 15 monomers, 4628.993 Da Detail

TAATTAACTA TATTA

3. SILVER ION (non-polymer), 107.868 Da

Total weight

9365.8545 Da

Max. entity weight

4628.993 Da

Entity Connection

metal coordination 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:DC8:N3	3:AG1:AG
2	metal coordination	sing	2:DC8:N3	3:AG1:AG

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 68.1 %, Completeness (bb): 57.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	68.1 % (196 of 288)	68.1 % (196 of 288)
Suger, PO4	57.1 % (120 of 210)	57.1 % (120 of 210)
Nucleobase	97.4 % (76 of 78)	97.4 % (76 of 78)
Aromatic	96.7 % (58 of 60)	96.7 % (58 of 60)
Methyl	100.0 % (14 of 14)	100.0 % (14 of 14)

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

TAATATACTT AATTA

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

TAATTAACTA TATTA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPAPAPTPAPTPAPCPTPTPAPAPTPTP*A)-3')	natural abundance	DNA	2 mM
2	DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3')	natural abundance	DNA	2 mM
3	AgNO3	natural abundance		2.1 mM
4	NaNO3	natural abundance	salt	100 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
7	DNA (5'-D(TPAPAPTPAPTPAPCPTPTPAPAPTPTP*A)-3')	natural abundance	DNA	2 mM
8	DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3')	natural abundance	DNA	2 mM
9	AgNO3	natural abundance		2.1 mM
10	NaNO3	natural abundance	salt	100 mM
11	D2O	[U-2H]	solvent	100 %

Release date

2016-08-21

Citation

Structure Determination of an Ag^I -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with ¹ H/¹⁵ N/¹⁰⁹ Ag NMR Spectroscopy
Dairaku, T., Furuita, K., Sato, H., Sebera, J., Nakashima, K., Kondo, J., Yamanaka, D., Kondo, Y., Okamoto, I., Ono, A., Sychrovsky, V., Kojima, C., Tanaka, Y.
Chemistry (2016), PubMed 27505707 , DOI 10.1002/chem.201603048 , Abstract

Related entities 2. DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11608_2rvp.nef
Input source #2: Coordindates	2rvp.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:8:DC:N3	3:1:AG:AG	unknown	unknown	n/a
1:8:DC:N3	3:1:AG:AG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	AG	SILVER ION	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	15	0	0	100.0
2	2	15	0	0	100.0

Content subtype: combined_11608_2rvp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	244		100.0 (chain: 1, length: 15), 100.0 (chain: 2, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	222 (1)	noe	93.3 (chain: 1, length: 15), 93.3 (chain: 2, length: 15)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	84 (1)	hbond	93.3 (chain: 1, length: 15), 93.3 (chain: 2, length: 15)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	236 (236)	.	100.0 (chain: 1, length: 15), 100.0 (chain: 2, length: 15)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 15, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 15, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 244
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	DA	H62	7.23
3	DA	H61	6.21
5	DA	H62	7.35
5	DA	H61	6.21
7	DA	H62	7.3
7	DA	H61	6.28
11	DA	H62	7.35
11	DA	H61	6.2
12	DA	H62	7.16
12	DA	H61	6.12

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	144	98	68.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	60	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
18	DA	H62	7.23
18	DA	H61	6.22
21	DA	H62	7.35
21	DA	H61	6.16
22	DA	H62	7.19
22	DA	H61	6.05
25	DA	H62	7.37
25	DA	H61	6.29
27	DA	H62	7.32
27	DA	H61	6.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	144	98	68.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	60	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 15, Sequence coverage: 93.3%
  - Entity_assembly_ID: 2, Chain length: 15, Sequence coverage: 93.3%
- Total number of restraints: 222
- Weight of restraints: 1.0 (222)
- Potential type of restraints: square-well-parabolic (222)
- Range of distance target values: 1.91, 6.26 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
  - Chain_ID: A
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: 1, Chain length: 15, Sequence coverage: 93.3%
    - Entity_assembly_ID: 2, Chain length: 15, Sequence coverage: 93.3%
  - Total number of restraints: 84
  - Weight of restraints: 1.0 (84)
  - Potential type of restraints: square-well-parabolic (84)
  - Range of distance target values: 1.87, 3.69 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: 1
    - Chain_ID: 2
    - Chain_ID: A
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 15, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 236
- Total number of restraints per polymer type: 236
- Weight of restraints: 1.0 (236)
- Potential type of restraints: square-well-parabolic (236)
- Dihedral angle restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2

Keywords C-Ag(I)-C BASE-PAIR, DNA, METALLO-BASE-PAIR, METALLO-DNA

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Found 1 Document (0.379 seconds)

BMRB: 11608

Sample #1

Sample #2

Related entities 2. DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.379 seconds)

BMRB: 11608

Sample #1

Sample #2

Related entities 2. DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail

Related entities 2. DNA (5'-D(TPAPAPTPTPAPAPCPTPAPTPAPTPTP*A)-3'), : 1 entities Detail