BMRBj - BMREntryMaster

Found 1 Document (0.386 seconds)

BMRB: 18454

2LT0

NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein

Authors

Zaliznyak, T., de los Santos, C., Lukin, M., El-khateeb, M., Bonala, R., Johnson, F.

Assembly

11 mer oligonucleotide-B

Entity

1. 11 mer oligonucleotide-B (polymer, Thiol state: not present), 11 monomers, 3397.158 Da Detail

CGTACGCATG C

2. 11 mer oligonucleotide-D (polymer, Thiol state: not present), 11 monomers, 3461.207 Da Detail

GCATGAGTAC G

Total weight

6858.365 Da

Max. entity weight

3461.207 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 66.4 %, Completeness (bb): 68.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	66.4 % (142 of 214)	66.4 % (142 of 214)
Suger, PO4	68.2 % (105 of 154)	68.2 % (105 of 154)
Nucleobase	61.7 % (37 of 60)	61.7 % (37 of 60)
Aromatic	75.0 % (33 of 44)	75.0 % (33 of 44)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. 11 mer oligonucleotide-B

CGTACGCATG C

2. 11 mer oligonucleotide-D

GCATGAGTAC G

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	11_mer_oligonucleotide-B	natural abundance		0.5 mM
2	D2O	natural abundance		100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.6

#	Name	Isotope labeling	Concentration
3	11_mer_oligonucleotide-B	natural abundance	0.5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

Release date

2012-06-10

Citation

NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein
Zaliznyak, T., de los Santos, C., Lukin, M., El-khateeb, M., Bonala, R., Johnson, F.
Biopolymers (2010), 93, 391-401, PubMed 20049919 , DOI 10.1002/bip.21366 , Abstract

Related entities 2. 11 mer oligonucleotide-D, : 2 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18454_2lt0.nef
Input source #2: Coordindates	2lt0.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'	1:6:63G:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	6	63G	(6S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one	Coordinates

Sequence alignments

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

-------------10-
.....CGTACXCATGC
      ||||      
GCATGAGTACG-.-.-
--------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_18454_2lt0.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	Warning	142		90.9 (chain: B, length: 11), 100.0 (chain: D, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	524 (1)	noe	90.9 (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: 90.9%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 142
- Completeness of assignments
  - Entity_assemble_ID: D
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	72	68.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	54	70.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	18	64.3

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	10	10	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: 90.9%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 524
- Weight of restraints: 1.0 (524)
- Potential type of restraints: square-well-parabolic (524)
- Range of distance target values: 1.57, 7.64 (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 acrolein adducts, damaged DNA structure, DNA lesions, NMR

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Found 1 Document (0.386 seconds)

BMRB: 18454

Sample #1

Sample #2

Related entities 2. 11 mer oligonucleotide-D, : 2 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail