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Found 1 Document (0.35 seconds)

BMRB: 17885

2LIA

Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct

Authors

Szulik, M.W., Ganguly, M., Wang, R., Gold, B., Stone, M.P.

Assembly

DNA dodecamer

Entity

1. DNA dodecamer (polymer), 12 monomers, 3754.417 Da Detail

GAGAXCGCTC TC

Formula weight

3754.417 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 56.9 %, Completeness (bb): 55.8 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	56.9 % (62 of 109)	56.9 % (62 of 109)
Suger, PO4	55.8 % (43 of 77)	55.8 % (43 of 77)
Nucleobase	59.4 % (19 of 32)	59.4 % (19 of 32)
Aromatic	77.3 % (17 of 22)	77.3 % (17 of 22)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. DNA dodecamer

GAGAXCGCTC TC

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA dodecamer	[U-2H]	0.25 mM
2	sodium phosphate	natural abundance	10 mM
3	sodium chloride	natural abundance	200 mM
4	sodium azide	natural abundance	0.011 M
5	sodium EDTA	natural abundance	0.05 mM

Release date

2011-09-11

Citation

Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine
Szulik, M.W., Voehler, M.W., Ganguly, M., Gold, B., Stone, M.P.
Biochemistry (2013), 52, 7659-7668, PubMed 24131376 , DOI 10.1021/bi400695r , Abstract

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17885_2lia.nef
Input source #2: Coordindates	2lia.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)
1:4:DA:O3'	1:5:2LA:P	unknown	unknown	n/a
1:5:2LA:O3'	1:6:DC:P	unknown	unknown	n/a
2:4:DA:O3'	2:5:2LA:P	unknown	unknown	n/a
2:5:2LA:O3'	2:6:DC:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	5	2LA	2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one	Assigned chemical shifts, Coordinates
B	17	2LA	2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one	Coordinates

Sequence alignments

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

--------10--
GAGAXCGCTCTC
||||||||||||
GAGAXCGCTCTC

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

------20----
GAGAXCGCTCTC
||||||||||||
GAGAXCGCTCTC
--------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_17885_2lia.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	69		100.0 (chain: A, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	338 (1)	noe	91.7 (chain: A, length: 12), 91.7 (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: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
5	2LA

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	62	56.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	43	55.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	19	59.4

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 91.7%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%
- Total number of restraints: 338
- Weight of restraints: 1.0 (338)
- Potential type of restraints: upper-bound-parabolic (338)
- Range of distance target values: 1.62, 4.53 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords DNA

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Found 1 Document (0.35 seconds)

BMRB: 17885

Sample

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail