BMRBj - BMREntryMaster

Found 1 Document (0.445 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

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Found 1 Document (0.445 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