BMRBj - BMREntryMaster

Found 1 Document (0.228 seconds)

BMRB: 30759

Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site

Authors

Kellum Jr, A.H., Qiu, D., Voehler, M.W., Martin, W.J., Gates, K.S., Stone, M.P.

Assembly

DNA TATGTCTAAGTTCATCTA, DNA TAGATGAACXTAGACATA

Entity

1. DNA TATGTCTAAGTTCATCTA, DNA TAGATGAACXTAGACATA, entity 1 (polymer, Thiol state: not present), 18 monomers, 5543.547 Da Detail

TATGTCTAAG TTCATCTA

2. DNA TATGTCTAAGTTCATCTA, DNA TAGATGAACXTAGACATA, entity 2 (polymer, Thiol state: not present), 18 monomers, 5502.515 Da Detail

TAGATGAACX TAGACATA

Total weight

11046.0625 Da

Max. entity weight

5543.547 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 57.0 %, Completeness (bb): 56.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	57.0 % (192 of 337)	57.0 % (192 of 337)
Suger, PO4	56.3 % (138 of 245)	56.3 % (138 of 245)
Nucleobase	58.7 % (54 of 92)	58.7 % (54 of 92)
Aromatic	60.0 % (42 of 70)	60.0 % (42 of 70)
Methyl	100.0 % (12 of 12)	100.0 % (12 of 12)

1. entity 1

TATGTCTAAG TTCATCTA

2. entity 2

TAGATGAACX TAGACATA

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 500 uM deoxyribonucleic acid, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	deoxyribonucleic acid	natural abundance		500 (±0.2) uM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details 500 uM deoxyribonucleic acid, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	deoxyribonucleic acid	natural abundance		500 (±0.2) uM

Release date

2021-04-28

Citation

Structure of a Stable Interstrand DNA Cross-Link Involving a β-N-Glycosyl Linkage Between an N⁶-dA Amino Group and an Abasic Site
Kellum Jr, A.H., Qiu, D.Y., Voehler, M.W., Martin, W., Gates, K.S., Stone, M.P.
Biochemistry (2021), 60, 41-52, PubMed 33382597 , DOI 10.1021/acs.biochem.0c00596 , Abstract

Experiments performed 4 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30759_3.str
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
2	10	AAB	2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE	Assigned chemical shifts

Content subtype: bmr30759_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	196		100.0 (chain: 1, length: 18), 100.0 (chain: 2, length: 18)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 196
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	101	57.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	70	55.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	31	62.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	9	75.0

Comp_index_ID	Comp_ID
10	AAB

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	91	56.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	68	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	23	54.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	11	57.9

Keywords AP site, DNA, interstrand crosslink

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Found 1 Document (0.228 seconds)

BMRB: 30759

Sample #1

Sample #2

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail