BMRBj - BMREntryMaster

Found 1 Document (0.479 seconds)

BMRB: 18838

2M12

Solution structure of the ID3 stem loop of domain 1 in the ai5gamma group II intron

Authors

Popovic, M., Greenbaum, N.L.

Assembly

ID3 stem loop of domain 1 in the ai5gamma group II intron

Entity

1. ID3 stem loop of domain 1 in the ai5gamma group II intron (polymer, Thiol state: not present), 23 monomers, 7506.451 Da Detail

GGGUGUAUUG GAAAUGAGCA CCC

Formula weight

7506.451 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.3 %, Completeness (bb): 78.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	80.3 % (281 of 350)	75.6 % (149 of 197)	86.3 % (132 of 153)
Suger, PO4	78.3 % (198 of 253)	72.5 % (100 of 138)	85.2 % (98 of 115)
Nucleobase	85.6 % (83 of 97)	83.1 % (49 of 59)	89.5 % (34 of 38)
Aromatic	86.5 % (77 of 89)	84.3 % (43 of 51)	89.5 % (34 of 38)

1. ID3

GGGUGUAUUG GAAAUGAGCA CCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	ID3	natural abundance	0.03 ~ 0.9 mM
2	sodium chloride	natural abundance	60 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	ID3	natural abundance	0.03 ~ 0.9 mM
6	sodium chloride	natural abundance	60 mM
7	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
9	sodium chloride	natural abundance	60 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

Release date

2013-10-20

Citation

Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site
Popovic, M., Greenbaum, N.L.
RNA (2014), 20, 24-35, PubMed 24243113 , DOI 10.1261/rna.039701.113 , Abstract

Related entities 1. ID3 stem loop of domain 1 in the ai5gamma group II intron, : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	ID3	natural abundance	0.03 ~ 0.9 mM
6	sodium chloride	natural abundance	60 mM
7	D2O	natural abundance	100 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	ID3	natural abundance	0.03 ~ 0.9 mM
6	sodium chloride	natural abundance	60 mM
7	D2O	natural abundance	100 %

3 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
5	ID3	natural abundance	0.03 ~ 0.9 mM
6	sodium chloride	natural abundance	60 mM
7	D2O	natural abundance	100 %

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
9	sodium chloride	natural abundance	60 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

7 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
9	sodium chloride	natural abundance	60 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	ID3	[U-100% 13C; U-100% 15N]	0.3 ~ 0.5 mM
13	potassium chloride	natural abundance	60 mM
14	D2O	natural abundance	100 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	ID3	natural abundance	0.03 ~ 0.9 mM
2	sodium chloride	natural abundance	60 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18838_2m12.nef
Input source #2: Coordindates	2m12.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--------20---
GGGUGUAUUGGAAAUGAGCACCC
|||||||||||||||||||||||
GGGUGUAUUGGAAAUGAGCACCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	23	0	0	100.0

Content subtype: combined_18838_2m12.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	290		100.0 (chain: A, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	226 (1)	noe	100.0 (chain: A, length: 23)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 158
  - ¹³C chemical shifts: 132
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	H21	8.45
2	G	H22	6.017
3	G	H21	8.518
3	G	H22	6.098
5	G	H21	7.911
5	G	H22	5.957
18	G	H22	6.329
20	A	H61	8.146
20	A	H62	6.364

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	197	149	75.6
¹³C chemical shifts	153	132	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	100	72.5
¹³C chemical shifts	115	98	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	49	83.1
¹³C chemical shifts	38	34	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	17	85.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 100.0%
- Total number of restraints: 226
- Weight of restraints: 1.0 (226)
- Potential type of restraints: square-well-parabolic (226)
- Range of distance target values: 2.44, 5.8 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords ID3

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Found 1 Document (0.479 seconds)

BMRB: 18838

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. ID3 stem loop of domain 1 in the ai5gamma group II intron, : 1 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail