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BMRB: 30054

5J3I

NMR solution structure of [Sp, Sp]-PT dsDNA

Authors

Lan, W., Hu, Z., Cao, C.

Assembly

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

Entity

1. DNA (5'-D(*CP*GP*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3') (polymer, Thiol state: not present), 10 monomers, 3110.019 Da Detail

CGXCCGCCGA

2. DNA (5'-D(*TP*CP*GP*GP*CP*GP*(SSG)P*CP*CP*G)-3') (polymer, Thiol state: not present), 10 monomers, 3141.029 Da Detail

TCGGCGXCCG

Total weight

6251.048 Da

Max. entity weight

3141.029 Da

Source organism

Streptomyces lividans

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 45.0 %, Completeness: 31.7 %, Completeness (bb): 33.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	31.7 % (63 of 199)	30.4 % (55 of 181)	44.4 % (8 of 18)
Suger, PO4	33.3 % (48 of 144)	31.7 % (40 of 126)	44.4 % (8 of 18)
Nucleobase	27.3 % (15 of 55)	27.3 % (15 of 55)
Aromatic	38.9 % (14 of 36)	38.9 % (14 of 36)
Methyl	0.0 % (0 of 1)	0.0 % (0 of 1)

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

CGXCCGCCGA

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

TCGGCGXCCG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0, Details 1.0 mM Sp dsDNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Sp dsDNA	natural abundance	1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Chem. Shift Complete2

Sequence coverage: 45.0 %, Completeness: 30.4 %, Completeness (bb): 32.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	30.4 % (121 of 398)	29.0 % (105 of 362)	44.4 % (16 of 36)
Suger, PO4	32.3 % (93 of 288)	30.6 % (77 of 252)	44.4 % (16 of 36)
Nucleobase	25.5 % (28 of 110)	25.5 % (28 of 110)
Aromatic	37.5 % (27 of 72)	37.5 % (27 of 72)
Methyl	0.0 % (0 of 2)	0.0 % (0 of 2)

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

CGXCCGCCGA

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

TCGGCGXCCG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0, Details 1.0 mM Sp dsDNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Sp dsDNA	natural abundance	1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Release date

2016-11-13

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: 30053 released on 2016-06-19
    Title Solution NMR structure of PT-free dsDNA from Streptomyces lividans

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30054_5j3i.nef
Input source #2: Coordindates	5j3i.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)
1:2:DG:O3'	1:3:GS:P	unknown	unknown	n/a
1:3:GS:O3'	1:4:DC:P	unknown	unknown	n/a
2:6:DG:O3'	2:7:GS:P	unknown	unknown	n/a
2:7:GS:O3'	2:8:DC:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	GS	GUANOSINE-5'-THIO-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates
B	17	GS	GUANOSINE-5'-THIO-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10
CGXCCGCCGA
||||||||||
CGXCCGCCGA

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

--------20
TCGGCGXCCG
||||||||||
TCGGCGXCCG
--------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_30054_5j3i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	67		100.0 (chain: A, length: 10)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	63		100.0 (chain: B, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	419 (1)	noe	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 58
  - ³¹P chemical shifts: 9
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 54
  - ³¹P chemical shifts: 9
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
3	GS

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	P	3.808
4	DC	P	3.467
5	DC	P	4.136
6	DG	P	4.014
7	DC	P	3.49
8	DC	P	4.013
9	DG	P	3.875
10	DA	P	3.771

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	55	60.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	40	63.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	15	53.6

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

Comp_index_ID	Comp_ID
17	GS

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	DC	P	3.614
13	DG	P	4.014
14	DG	P	3.817
15	DC	P	3.537
16	DG	P	3.607
18	DC	P	4.007
19	DC	P	3.601
20	DG	P	4.132

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	50	55.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	37	58.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	13	48.1

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	4	4	100.0

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: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 419
- Weight of restraints: 1.0 (419)
- Potential type of restraints: square-well-parabolic (419)
- Range of distance target values: 2.35, 4.4 (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 DNA, Sp]-PT dsDNA, [Sp

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Found 1 Document (0.449 seconds)

BMRB: 30054

Sample

Sample

Entries sharing articles BMRB: 2 entries Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

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Instrument

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NMR combined restraints 4 contents Detail