BMRBj - BMREntryMaster

Found 1 Document (0.373 seconds)

BMRB: 17814

2LGM

Structure of DNA Containing an Aristolactam II-dA Lesion.

Authors

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

Assembly

DNA Containing an Aristolactam II-dA Lesion

Entity

1. DNA Containing an Aristolactam II-dA Lesion (polymer, Thiol state: not present), 11 monomers, 3452.193 Da Detail

GCATGTGTAC G

Formula weight

3452.193 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 71.7 %, Completeness (bb): 75.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	71.7 % (76 of 106)	71.7 % (76 of 106)
Suger, PO4	75.3 % (58 of 77)	75.3 % (58 of 77)
Nucleobase	62.1 % (18 of 29)	62.1 % (18 of 29)
Aromatic	68.2 % (15 of 22)	68.2 % (15 of 22)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA 11m dupl ALII

GCATGTGTAC G

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DNA 11m dupl ALII	natural abundance	0.25 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM
4	D2O	natural abundance	100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	DNA 11m dupl ALII	natural abundance	0.25 mM
6	sodium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	50 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

Release date

2011-11-30

Citation

Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts
Lukin, M., Zaliznyak, T., Johnson, F., de Los Santos, C.
Nucleic Acids Res. (2012), 40, 2759-2770, PubMed 22121223 , DOI 10.1093/nar/gkr1094 , 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_17814_2lgm.nef
Input source #2: Coordindates	2lgm.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)
1:6:DA:N6	3:1:A4A:C7	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	A4A	[1,3]benzodioxolo[6,5,4-cd]benzo[f]indol-5(6H)-one	Distance restraints

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	11	0	0	100.0
2	2	11	0	0	100.0

Content subtype: combined_17814_2lgm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	76		100.0 (chain: 2, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	647 (1)	noe	100.0 (chain: 1, length: 11), 100.0 (chain: 2, length: 11), 100.0 (chain: A, length: 1)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	76	71.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	58	75.3

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: 1, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: A, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 647
- Weight of restraints: 1.0 (647)
- Potential type of restraints: square-well-parabolic (647)
- Range of distance target values: 1.02, 9.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: 1
  - Chain_ID: 2
  - Chain_ID: A
- Distance restraints on contact map

Keywords Aristolactam-II adduct, DNA Structure, Duplex Stability, NER Recognition, NMR

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 (0.373 seconds)

BMRB: 17814

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail