BMRBj - BMREntryMaster

Found 1 Document (0.312 seconds)

BMRB: 16980

2KYD

RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width

Authors

Tolbert, B.S., Summers, M.F., Miyazaki, Y., Barton, S., Kinde, B., Stark, P., Singh, R., Bax, A., Case, D.

Assembly

5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3'

Entity

1. 5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3' (polymer, Thiol state: not present), 29 monomers, 9326.461 × 2 Da Detail

GCGGUACUAG UUAGCUAACU AGCUUUGUA

Total weight

18652.922 Da

Max. entity weight

9326.461 Da

Source organism

Murine leukemia virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 30.6 %, Completeness (bb): 16.1 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	30.6 % (77 of 252)	30.6 % (77 of 252)
Suger, PO4	16.1 % (28 of 174)	16.1 % (28 of 174)
Nucleobase	62.8 % (49 of 78)	62.8 % (49 of 78)
Aromatic	72.1 % (49 of 68)	72.1 % (49 of 68)

1. RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3')

GCGGUACUAG UUAGCUAACU AGCUUUGUA

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

Release date

2010-07-25

Citation

Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement
Tolbert, B.S., Miyazaki, Y., Barton, S., Kinde, B., Starck, P., Singh, R., Bax, A., Case, D.A., Summers, M.F.
J. Biomol. NMR (2010), 47, 205-219, PubMed 20549304 , DOI 10.1007/s10858-010-9424-x , Abstract

Related entities 1. 5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3', : 1 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

2 2D 1H-1H TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

3 2D 1H-13C HMQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

4 2D Tr 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

5 2D Tr 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	natural abundance	0.25 ~ 1.0 mM
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[U-100% 13C], [C-100% 13C]	0.25 mM
3	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')	[G-100% 13C], [A-100% 13C]	0.25 mM
4	sodium chloride	natural abundance	150 mM
5	TRIS	natural abundance	10 mM
6	D2O	natural abundance	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16980_2kyd.nef
Input source #2: Coordindates	2kyd.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	Error

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------
CUAGUUAGCUAACUAG
||||||||||||||||
CUAGUUAGCUAACUAG

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

--20--------30--
CUAGUUAGCUAACUAG
||||||||||||||||
CUAGUUAGCUAACUAG
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	16	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_16980_2kyd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	65		No information
1	Distance restraints	AMBER_distance_constraints_2	OK	303 (1)	noe	100.0 (chain: A, length: 16), 100.0 (chain: B, length: 16)
2	Distance restraints	AMBER_distance_constraints_5	OK	316 (1)	undefined	100.0 (chain: A, length: 16), 100.0 (chain: B, length: 16)
3	Distance restraints	AMBER_distance_constraints_7	OK	76 (1)	hbond	100.0 (chain: A, length: 16), 100.0 (chain: B, length: 16)
1	Dihedral angle restraints	AMBER_dihedral_3	Warning	47 (47)	.	25.0 (chain: A, length: 16)
1	RDC restraints	AMBER_dipolar_coupling_6	OK	42 (42)	.	93.8 (chain: A, length: 16), 93.8 (chain: B, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 303
- Weight of restraints: 1.0 (303)
- Potential type of restraints: square-well-parabolic (303)
- Range of distance target values: 2.5, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: AMBER_distance_constraints_5
  - Status: OK
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
  - Total number of restraints: 10
  - Weight of restraints: 1.0 (10)
  - Potential type of restraints: square-well-parabolic (10)
  - Range of distance target values: 1.67, 1.86 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: AMBER_distance_constraints_7
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
      - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
    - Total number of restraints: 76
    - Weight of restraints: 1.0 (76)
    - Potential type of restraints: square-well-parabolic (76)
    - Range of distance target values: 2.1, 2.65 (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: AMBER_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 25.0%
- Total number of restraints: 47
- Total number of restraints per polymer type: 47
- Weight of restraints: 1.0 (47)
- Potential type of restraints: square-well-parabolic (47)
- Dihedral angle restraints per residue

RDC restraints

Saveframe: AMBER_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 93.8%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of restraints: 42
- Potential type of restraints: square-well-parabolic (42)
- Range of observed RDC values: 28.4, 49.4 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None

Keywords A-form RNA, Moloney Murine Leukemia Virus Dimerization Signal, RDC and RCSA refinement, SLB duplex

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 (0.312 seconds)

BMRB: 16980

Sample

Related entities 1. 5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3', : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail

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 (0.312 seconds)

BMRB: 16980

Sample

Related entities 1. 5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3', : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail

Related entities 1. 5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3', : 1 entities Detail