BMRBj - BMREntryMaster

Found 1 Document (0.458 seconds)

BMRB: 15858

2K65

NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)

Authors

Kruschel, D., Sigel, R.K. O.

Assembly

29-MER

Entity

1. RNA (7A-MER) (polymer, Thiol state: not present), 7 monomers, 2299.367 Da Detail

GGCACUG

2. RNA (7B-MER) (polymer, Thiol state: not present), 7 monomers, 2260.327 Da Detail

CAGUGUC

Total weight

4559.694 Da

Max. entity weight

2299.367 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 66.7 %, Completeness (bb): 53.2 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	66.7 % (144 of 216)	87.8 % (108 of 123)	38.7 % (36 of 93)
Suger, PO4	53.2 % (82 of 154)	82.1 % (69 of 84)	18.6 % (13 of 70)
Nucleobase	100.0 % (62 of 62)	100.0 % (39 of 39)	100.0 % (23 of 23)
Aromatic	100.0 % (54 of 54)	100.0 % (31 of 31)	100.0 % (23 of 23)

1. RNA (7A-MER)

GGCACUG

2. RNA (7B-MER)

CAGUGUC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
1	RNA (7A-MER)	natural abundance	0.8-0.9 mM
2	RNA (7B-MER)	natural abundance	0.8-0.9 mM
3	potassium chloride	natural abundance	100 mM
4	EDTA	natural abundance	10 uM
5	D2O	[U-100% 2H]	100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K

#	Name	Isotope labeling	Concentration
6	RNA (7A-MER)	natural abundance	0.9 mM
7	RNA (7B-MER)	natural abundance	0.9 mM
8	potassium chloride	natural abundance	100 mM
9	EDTA	natural abundance	10 uM
10	H2O	natural abundance	90 %
11	D2O	[U-100% 2H]	10 %

Release date

2009-10-11

Citation

NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition
Kruschel, D., Sigel, R.K. O.
RNA (2014), 20, 295-307, PubMed 24448450 , DOI 10.1261/rna.041137.113 , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15858_2k65.nef
Input source #2: Coordindates	2k65.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

-------
GGCACUG
|||||||
GGCACUG

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

-60----
CAGUGUC
|||||||
CAGUGUC
-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	7	0	0	100.0
B	B	7	0	0	100.0

Content subtype: combined_15858_2k65.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	153		100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	221 (1)	noe	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	60 (1)	noe	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)
3	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	37 (1)	noe	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_9	OK	62 (62)	.	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_11	OK	39 (39)	.	85.7 (chain: A, length: 7), 100.0 (chain: B, length: 7)
3	Dihedral angle restraints	CNS/XPLOR_dihedral_13	OK	14 (14)	.	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 117
  - ¹³C chemical shifts: 36
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
14	G	H21	7.521
14	G	H22	6.053
16	A	H61	7.705
16	A	H62	6.056

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	53	86.9
¹³C chemical shifts	46	17	37.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	34	81.0
¹³C chemical shifts	35	6	17.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0
¹³C chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	5	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
60	A	H62	6.183
61	G	H21	8.069
61	G	H22	5.934
63	G	H21	7.587
63	G	H22	5.792

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	55	88.7
¹³C chemical shifts	47	19	40.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	35	83.3
¹³C chemical shifts	35	7	20.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	12	12	100.0

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
- Total number of restraints: 221
- Weight of restraints: 1.0 (221)
- Potential type of restraints: square-well-parabolic (221)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
  - Total number of restraints: 60
  - Weight of restraints: 1.0 (60)
  - Potential type of restraints: square-well-parabolic (60)
  - Range of distance target values: 2.4, 5.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_7
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
      - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
    - Total number of restraints: 37
    - Weight of restraints: 1.0 (37)
    - Potential type of restraints: square-well-parabolic (37)
    - Range of distance target values: 1.95, 2.95 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_9
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
- Total number of restraints: 62
- Total number of restraints per polymer type: 62
- Weight of restraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (62)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Saveframe: CNS/XPLOR_dihedral_11
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 85.7%
    - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
  - Total number of restraints: 39
  - Total number of restraints per polymer type: 39
  - Weight of restraints: 1.0 (39)
  - Potential type of restraints: square-well-parabolic (39)
  - Dihedral angle restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Saveframe: CNS/XPLOR_dihedral_13
    - Status: OK
    - Experiment type: .
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
      - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
    - Total number of restraints: 14
    - Total number of restraints per polymer type: 14
    - Weight of restraints: 1.0 (14)
    - Potential type of restraints: square-well-parabolic (14)
    - Dihedral angle restraints per residue
      - Chain_ID: A
      - Chain_ID: B

Keywords duplex, EBS1, exon binding site 1, group II intron, IBS1, intron binding site 1, NMR, ribozyme, RNA 7-mer, splicing

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 (0.458 seconds)

BMRB: 15858

Sample #1

Sample #2

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail