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BMRB: 19912

2MNX

MAJOR GROOVE ORIENTATION OF THE (2S)-N6-(2-HYDROXY-3-BUTEN-1-YL)-2'-DEOXYADENOSINE DNA ADDUCT INDUCED BY 1,2-EPOXY-3-BUTENE

Authors

Kowal, E.A., Kotapati, S., Turo, M., Tretyakova, N., Stone, M.P.

Assembly

DNA duplex

Entity

1. DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3') (polymer, Thiol state: not present), 11 monomers, 3549.325 Da Detail

CGGACXAGAA G

2. DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') (polymer, Thiol state: not present), 11 monomers, 3354.117 Da Detail

CTTCTTGTCC G

Total weight

6903.442 Da

Max. entity weight

3549.325 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, homonucl_NOEs

Chem. Shift Complete1

Sequence coverage: 95.5 %, Completeness: 58.3 %, Completeness (bb): 57.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	58.3 % (120 of 206)	58.3 % (120 of 206)
Suger, PO4	57.1 % (84 of 147)	57.1 % (84 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. DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3')

CGGACXAGAA G

2. DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')

CTTCTTGTCC G

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPGPGPAPCP(6HB)PAPGPAPAP*G)-3')	natural abundance	0.51 mM
2	DNA (5'-D(CPTPTPCPTPTPGPTPCPCP*G)-3')	natural abundance	0.51 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	50 uM
5	sodium phosphate (pH 7)	natural abundance	10 mM
6	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 72.7 %, Completeness: 34.0 %, Completeness (bb): 28.6 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	34.0 % (140 of 412)	34.0 % (140 of 412)
Suger, PO4	28.6 % (84 of 294)	28.6 % (84 of 294)
Nucleobase	47.5 % (56 of 118)	47.5 % (56 of 118)
Aromatic	51.2 % (43 of 84)	51.2 % (43 of 84)
Methyl	50.0 % (5 of 10)	50.0 % (5 of 10)

1. DNA (5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3')

CGGACXAGAA G

2. DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')

CTTCTTGTCC G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7

#	Name	Isotope labeling	Concentration
7	DNA (5'-D(CPGPGPAPCP(6HB)PAPGPAPAP*G)-3')	natural abundance	0.51 mM
8	DNA (5'-D(CPTPTPCPTPTPGPTPCPCP*G)-3')	natural abundance	0.51 mM
9	sodium chloride	natural abundance	100 mM
10	EDTA	natural abundance	50 uM
11	sodium phosphate (pH 7)	natural abundance	10 mM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %

Release date

2014-10-05

Citation

Major groove orientation of the (2S)-N(6)-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene
Kowal, E.A., Kotapati, S., Turo, M., Tretyakova, N., Stone, M.P.
Chem. Res. Toxicol. (2014), 27, 1675-1686, PubMed 25238403 , DOI 10.1021/tx500159w , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19912_2mnx.nef
Input source #2: Coordindates	2mnx.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'	1:6:6HB:P	unknown	unknown	n/a
1:6:6HB:O3'	1:7:DA:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	6HB	2'-deoxy-N-[(2S)-2-hydroxybut-3-en-1-yl]adenosine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10-
CGGACXAGAAG
|||||||||||
CGGACXAGAAG

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

-------20--
CTTCTTGTCCG
|||||||||||
CTTCTTGTCCG
--------10-

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_19912_2mnx.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	132		100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)
2	Assigned chemical shifts	assigned_chem_shift_list_2	OK	21		81.8 (chain: A, length: 11), 72.7 (chain: B, length: 11)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	230 (1)	noe	90.9 (chain: A, length: 11), 90.9 (chain: B, length: 11)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	42 (1)	hbond	90.9 (chain: A, length: 11), 90.9 (chain: B, length: 11)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	66 (66)	.	81.8 (chain: A, length: 11), 90.9 (chain: B, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- 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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 132
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chem_shift_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 81.8%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 72.7%
- Total number of assignments
  - ¹H chemical shifts: 21
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
6	6HB

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	56	59.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	40	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	16	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	64	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	44	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	20	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

Comp_index_ID	Comp_ID
6	6HB

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	9	9.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	9	37.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	4	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	11	9.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	11	31.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 90.9%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
- Total number of restraints: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: upper-bound-parabolic (230)
- Range of distance target values: 1.4, 5.03 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 90.9%
    - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: upper-bound-parabolic (42)
  - Range of distance target values: 1.71, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 81.8%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords 11 mer, 1, 2-EPOXY-3-BUTENE, (2S)-N6-(2-HYDROXY-3-BUTEN-1-YL)-2'-DEOXYADENOSINE ADDUCT, B-form DNA

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Found 1 Document (0.44 seconds)

BMRB: 19912

Sample

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail