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Found 1 Document (0.358 seconds)

BMRB: 18430

2LSF

Structure and Stability of Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine: An Oxidative Lesion Repair by NER.

Authors

Zaliznyak, T., de los Santos, C., Lukin, M.

Assembly

Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine

Entity

1. 11 mer oligonucleotide B (polymer, Thiol state: not present), 11 monomers, 3379.143 Da Detail

CGTACXCATG C

2. 11 mer oligonucleotide D (polymer, Thiol state: not present), 11 monomers, 3452.193 Da Detail

GCATGTGTAC G

Total weight

6831.336 Da

Max. entity weight

3452.193 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 64.1 %, Completeness (bb): 65.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	64.1 % (132 of 206)	64.1 % (132 of 206)
Suger, PO4	65.3 % (96 of 147)	65.3 % (96 of 147)
Nucleobase	61.0 % (36 of 59)	61.0 % (36 of 59)
Aromatic	73.8 % (31 of 42)	73.8 % (31 of 42)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. 11 mer oligonucleotide B

CGTACXCATG C

2. 11 mer oligonucleotide D

GCATGTGTAC G

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	11 mer DNA duplex	natural abundance	0.7 mM
2	11 mer DNA duplex	natural abundance	0.7 mM
3	D2O	natural abundance	100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7

#	Name	Isotope labeling	Concentration
4	11 mer DNA duplex	natural abundance	0.7 mM
5	11 mer DNA duplex	natural abundance	0.7 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Release date

2012-09-09

Citation

Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER
Zaliznyak, T., Lukin, M., de los Santos, C.
Chem. Res. Toxicol. (2012), 25, 2103-2111, PubMed 22928555 , DOI 10.1021/tx300193k , Abstract

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18430_2lsf.nef
Input source #2: Coordindates	2lsf.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)
1:5:DC:O3'	1:6:02I:P	unknown	unknown	n/a
1:6:02I:O3'	1:7:DC:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	6	02I	(6S,7S,8S,10R)-4-amino-8-hydroxy-7,8,9,10-tetrahydro-6H-7,10-epoxyazepino[1,2-e]purin-6-yl dihydrogen phosphate	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

-------------10-
.....CGTACXCATGC
      ||||      
GCATGTGTACG-.-.-
--------10- - -

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	11	0	0	100.0
D	D	11	0	0	100.0

Content subtype: combined_18430_2lsf.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	Warning	139		100.0 (chain: B, length: 11), 100.0 (chain: D, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	543 (1)	noe	100.0 (chain: B, length: 11), 100.0 (chain: D, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 139
- Completeness of assignments
  - Entity_assemble_ID: B
  - Entity_assemble_ID: D
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
6	02I

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	63	63.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	45	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	18	60.0

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	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	69	65.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	51	66.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	18	62.1

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 543
- Weight of restraints: 1.0 (543)
- Potential type of restraints: square-well-parabolic (543)
- Range of distance target values: 1.57, 22.2 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: B
  - Chain_ID: D
- Distance restraints on contact map

Keywords (5 S) 5, 8-Cyclo-2 -Deoxyadenosine, NER, NMR, restrained molecular dynamics, solution structure

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Found 1 Document (0.358 seconds)

BMRB: 18430

Sample #1

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Experiments performed 5 experiments Detail

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NMR combined restraints 3 contents Detail