BMRBj - BMREntryMaster

Found 1 Document (1.418 seconds)

BMRB: 6756

2AHT

Solution structure of domain 6 from the ai5(gamma) group II intron

Authors

Erat, M.C., Sigel, R.K.O.

Assembly

D6short

Entity

1. Domain 6 (polymer, Thiol state: not present), 27 monomers, 8783.202 Da Detail

GGAGCGGGGG UGUAAACCUA UCGCUCC

2. MG (non-polymer), 24.305 Da

Total weight

8807.507 Da

Max. entity weight

8783.202 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.4 %, Completeness (bb): 84.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	87.4 % (375 of 429)	94.0 % (221 of 235)	79.9 % (143 of 179)	73.3 % (11 of 15)
Suger, PO4	84.5 % (251 of 297)	92.6 % (150 of 162)	74.8 % (101 of 135)
Nucleobase	93.9 % (124 of 132)	97.3 % (71 of 73)	95.5 % (42 of 44)	73.3 % (11 of 15)
Aromatic	93.2 % (110 of 118)	96.6 % (57 of 59)	95.5 % (42 of 44)	73.3 % (11 of 15)

1. Domain 6

GGAGCGGGGG UGUAAACCUA UCGCUCC

Show sample condition

Sample

Temperature 303 (±0.0) K, pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Release date

2007-03-28

Citation

Solution structure of domain 6 from a self-splicing group II intron ribozyme: a Mg(2+) binding site is located close to the stacked branch adenosine
Erat, M.C., Zerbe, O., Fox, T., Sigel, R.K.O.
Chembiochem. (2007), 8, 306-314, PubMed 17200997 , DOI 10.1002/cbic.200600459 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34199 released on 2018-01-10
Title Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding

Related entities 1. Domain 6, : 1 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H1H Noesy in D2O and H2O

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

2 2D 1H1H Tocsy

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

3 13C1H HSQC

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

4 15N1H HSQC

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

5 HCCH-Tocsy

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

6 HCCH-Cosy

Instrument

#1 Model Bruker AVANCE (700 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

pH 6.8 (±0.1)

#	Name	Concentration
1	Domain 6	0.6 mM
2	D2O	99.999 %
3	KCL	100 mM
4	EDTA	10 uM

Sample #2

pH 6.8 (±0.1)

#	Name	Concentration
5	Domain 6	0.6 mM
6	D2O	10 %
7	H2O	90 %
8	KCL	100 mM
9	EDTA	10 uM

Sample #3

pH 6.8 (±0.1)

#	Name	Isotope labeling	Concentration
10	Domain 6	[U-13C; U-15N]	0.6 mM
11	D2O		99.999 %
12	KCL		100 mM
13	EDTA		10 uM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6756_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

None

Content subtype: bmr6756_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	389		100.0 (chain: 1, length: 27)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 235
  - ¹³C chemical shifts: 143
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	H22	6.384
3	A	H61	8.002
3	A	H62	7.064
4	G	H21	8.571
4	G	H22	6.297
6	G	H21	8.03
8	G	H21	6.552
9	G	H21	8.547
9	G	H22	6.374
10	G	H21	8.656
10	G	H22	6.335
16	A	H61	7.946
16	A	H62	6.899
23	G	H22	6.143

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	235	221	94.0
¹³C chemical shifts	179	143	79.9
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	150	92.6
¹³C chemical shifts	135	101	74.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	71	97.3
¹³C chemical shifts	44	42	95.5
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	20	100.0

Keywords branch-point A, domain 6, magnesium binding sites, RNA hairpin, A-form helix, single nucleotide bulge, tetraloop, magnesium, metal ion binding

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Found 1 Document (1.418 seconds)

BMRB: 6756

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Domain 6, : 1 entities Detail

Experiments performed 6 experiments Detail

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Chemical shift validation 4 contents Detail