BMRBj - BMREntryMaster

Found 1 Document (0.47 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

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 (0.47 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail