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Found 1 Document (0.386 seconds)

BMRB: 30053

5J3G

Solution NMR structure of PT-free dsDNA from Streptomyces lividans

Authors

Lan, W., Cao, C.

Assembly

DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3')

Entity

1. DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3') (polymer, Thiol state: not present), 10 monomers, 3093.953 Da Detail

CGGCCGCCGA

2. DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3') (polymer, Thiol state: not present), 10 monomers, 3124.963 Da Detail

TCGGCGGCCG

Total weight

6218.916 Da

Max. entity weight

3124.963 Da

Source organism

Streptomyces lividans

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 50.0 %, Completeness: 39.7 %, Completeness (bb): 40.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	39.7 % (87 of 219)	39.2 % (78 of 199)	45.0 % (9 of 20)
Suger, PO4	40.0 % (64 of 160)	39.3 % (55 of 140)	45.0 % (9 of 20)
Nucleobase	39.0 % (23 of 59)	39.0 % (23 of 59)
Aromatic	40.0 % (16 of 40)	40.0 % (16 of 40)
Methyl	0.0 % (0 of 1)	0.0 % (0 of 1)

1. DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3')

CGGCCGCCGA

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

TCGGCGGCCG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.002), Details 1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Chem. Shift Complete2

Sequence coverage: 50.0 %, Completeness: 39.3 %, Completeness (bb): 40.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	39.3 % (172 of 438)	39.2 % (156 of 398)	40.0 % (16 of 40)
Suger, PO4	40.3 % (129 of 320)	40.4 % (113 of 280)	40.0 % (16 of 40)
Nucleobase	36.4 % (43 of 118)	36.4 % (43 of 118)
Aromatic	36.3 % (29 of 80)	36.3 % (29 of 80)
Methyl	0.0 % (0 of 2)	0.0 % (0 of 2)

1. DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3')

CGGCCGCCGA

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

TCGGCGGCCG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.002), Details 1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Release date

2016-06-19

Citation

Structural investigation into physiological DNA phosphorothioate modification
Lan, W., Hu, Z., Cao, C.
Sci. Rep. (2016), 6, 25737-25737, PubMed 27169778 , DOI 10.1038/srep25737 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30052 released on 2016-11-13
    Title NMR solution structure of [Rp, Rp]-PT dsDNA
  BMRB: 30054 released on 2016-11-13
    Title NMR solution structure of [Sp, Sp]-PT dsDNA

Experiments performed 5 experiments Detail

1 2D NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.002), Details 1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Agilent DD2 - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.0001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.01), Details 1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 2D DQF-COSY

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 2D NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 2D 1H-31P hetcor

Instrument

Agilent DD2 - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NaCl	natural abundance	100 mM
2	NaPO4	natural abundance	40 mM
3	PT-free dsDNA	none	1.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30053_5j3g.nef
Input source #2: Coordindates	5j3g.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10
CGGCCGCCGA
||||||||||
CGGCCGCCGA

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

--------20
TCGGCGGCCG
||||||||||
TCGGCGGCCG
--------10

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	10	0	0	100.0
B	B	10	0	0	100.0

Content subtype: combined_30053_5j3g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	87		100.0 (chain: A, length: 10)
2	Assigned chemical shifts	assigned_chemical_shifts_2	OK	85		100.0 (chain: B, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	495 (1)	noe	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 78
  - ³¹P chemical shifts: 9
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 78
  - ³¹P chemical shifts: 7
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	3.734
3	DG	P	3.843
4	DC	P	3.586
5	DC	P	3.609
6	DG	P	3.634
7	DC	P	3.621
8	DC	P	3.623
9	DG	P	3.859
10	DA	P	3.761

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	78	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	55	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	23	76.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	DC	P	3.602
13	DG	P	3.992
14	DG	P	3.681
15	DC	P	3.55
16	DG	P	3.796
17	DG	P	3.812
20	DG	P	3.968

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	78	78.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	58	82.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	20	69.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	4	80.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 495
- Weight of restraints: 1.0 (495)
- Potential type of restraints: square-well-parabolic (495)
- Range of distance target values: 2.35, 4.9 (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

Keywords dsDNA PT-free NMR Streptomyces lividans

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Found 1 Document (0.386 seconds)

BMRB: 30053

Sample

Sample

Entries sharing articles BMRB: 2 entries Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail