BMRBj - BMREntryMaster

Found 1 Document (0.267 seconds)

BMRB: 34390

A quadruplex hybrid structure with lpp loop orientation and 5 syn residues

Authors

Karg, B., Weisz, K.

Assembly

DNA (25-MER)

Entity

1. DNA (25-MER) (polymer, Thiol state: not present), 25 monomers, 8113.804 Da Detail

GCGTGGGTCA GGGTXGGTXG GACGC

Formula weight

8113.804 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 56.2 %, Completeness (bb): 45.3 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	56.2 % (123 of 219)	56.2 % (123 of 219)
Suger, PO4	45.3 % (73 of 161)	45.3 % (73 of 161)
Nucleobase	86.2 % (50 of 58)	86.2 % (50 of 58)
Aromatic	91.3 % (42 of 46)	91.3 % (42 of 46)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. entity 1

GCGTGGGTCA GGGTXGGTXG GACGC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.8 mM MYC4t-5s, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	MYC4t-5s	natural abundance		0.8 mM
2	potassium phosphate	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.8 mM MYC4t-5s, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	MYC4t-5s	natural abundance		0.8 mM
4	potassium phosphate	natural abundance		10 mM

Release date

2019-10-10

Citation

Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations
Karg, B., Mohr, S., Weisz, K.
Angew. Chem Int Ed Engl. (2019), 58, 11068-11071, PubMed 31134741 , DOI 10.1002/anie.201905372 , Abstract

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34390_3.str
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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	15	BGM	8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts
1	19	BGM	8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts

Content subtype: bmr34390_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	164		100.0 (chain: 1, length: 25)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 25, Sequence coverage: 100.0%

--------10--------20-----
GCGTGGGTCAGGGTXGGTXGGACGC
|||||||||||||||||||||||||
GCGTGGGTCAGGGTXGGTXGGACGC

Total number of assignments
- ¹H chemical shifts: 139
- ¹³C chemical shifts: 25

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
15	BGM
19	BGM

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C8	138.796
2	DC	C6	142.75
3	DG	C8	138.479
4	DT	C6	138.074
5	DG	C8	142.168
6	DG	C8	140.901
7	DG	C8	137.992
8	DT	C6	140.332
9	DC	C6	143.052
10	DA	C2	155.19
10	DA	C8	141.208
11	DG	C8	142.471
12	DG	C8	138.547
13	DG	C8	138.997
14	DT	C6	139.963
16	DG	C8	139.372
17	DG	C8	138.236
18	DT	C6	139.963
20	DG	C8	139.652
21	DG	C8	138.236
22	DA	C2	154.905
22	DA	C8	141.146
23	DC	C6	142.519
24	DG	C8	138.75
25	DC	C6	143.283

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	219	123	56.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	73	45.3

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	50	86.2

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0

Histogram of normalized assigned chemical shifts

Keywords DNA, G-quadruplex, duplex moiety, hybrid structure

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.267 seconds)

BMRB: 34390

Sample #1

Sample #2

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail