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BMRB: 18781

2LZW

DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link

Authors

Denisov, A.Y., McManus, F.P., Noronha, A.M., Wilds, C.J.

Assembly

DNA

Entity

1. DNA (polymer, Thiol state: not present), 11 monomers, 3436.194 × 2 Da Detail

CGAAAGTTTC G

2. HEPTANE (non-polymer, Thiol state: not present), 100.202 Da

Total weight

6972.5903 Da

Max. entity weight

3436.194 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.8 %, Completeness (bb): 71.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	69.8 % (74 of 106)	69.8 % (74 of 106)
Suger, PO4	71.4 % (55 of 77)	71.4 % (55 of 77)
Nucleobase	65.5 % (19 of 29)	65.5 % (19 of 29)
Aromatic	72.7 % (16 of 22)	72.7 % (16 of 22)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA

CGAAAGTTTC G

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	DNA	natural abundance		1 mM
2	D2O	natural abundance		100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
3	DNA	natural abundance	1 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

Release date

2013-10-13

Citation

Solution structures of DNA duplexes containing mispair-aligned O4U-heptylene-O4U and O6G-heptylene-O6G interstrand cross-links
Denisov, A.Y., McManus, F.P., O'Flaherty, D.K., Noronha, A.M., Wilds, C.J.
Biochemistry

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18781_2lzw.nef
Input source #2: Coordindates	2lzw.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)
2:6:DG:O6	3:1:HP6:C26	unknown	unknown	n/a
1:6:DG:O6	3:1:HP6:C20	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	HP6	HEPTANE	Assigned chemical shifts

Sequence alignments

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

--------10-
CGAAAGTTTCG
|||||||||||
CGAAAGTTTCG

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

--------10-
CGAAAGTTTCG
|||||||||||
CGAAAGTTTCG

Chain assignments

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

Content subtype: combined_18781_2lzw.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	82		100.0 (chain: B, length: 11), 100.0 (chain: C, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	145 (1)	noe	100.0 (chain: A, length: 11), 36.4 (chain: B, length: 11)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	87 (86)	.	100.0 (chain: A, 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: C, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	74	69.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	55	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	19	65.5

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	9	9	100.0

Comp_index_ID	Comp_ID
1	HP6

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 36.4%
- Total number of restraints: 145
- Weight of restraints: 1.0 (145)
- Potential type of restraints: lower-bound-parabolic (12), square-well-parabolic (133)
- Range of distance target values: 2.25, 4.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 86
- Total number of restraints per polymer type: 86
- Weight of restraints: 1.0 (86)
- Potential type of restraints: square-well-parabolic (86)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA DUPLEX, INTERSTRAND CROSS-LINK, NMR, SOLUTION STRUCTURE

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Found 1 Document (0.38 seconds)

BMRB: 18781

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail