BMRBj - BMREntryMaster

Found 1 Document (0.428 seconds)

BMRB: 18079

4A4R

UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops

Authors

Zhao, Q., Huang, H., Nagaswamy, U., Xia, Y., Gao, X., Fox, G.E.

Assembly

UNAC Tetraloops

Entity

1. UNAC Tetraloops (polymer, Thiol state: not present), 22 monomers, 7047.249 Da Detail

XGACCCGGCU AACGCUGGGU CC

Formula weight

7047.249 Da

Source organism

Haloarcula marismortui

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 47.1 %, Completeness (bb): 44.4 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	47.1 % (88 of 187)	47.1 % (88 of 187)
Suger, PO4	44.4 % (56 of 126)	44.4 % (56 of 126)
Nucleobase	52.5 % (32 of 61)	52.5 % (32 of 61)
Aromatic	71.1 % (32 of 45)	71.1 % (32 of 45)

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

XGACCCGGCU AACGCUGGGU CC

Show sample condition

Sample

Solvent system 99.96% D2O, Pressure 1 atm, Temperature 298.000 K, pH 7.000, Details 0.3 mM

#	Name	Isotope labeling	Type	Concentration
1	UNAC	[U-13C; U-15N]		0.3 mM
2	D2O	natural abundance		99.96 %

Release date

2012-05-21

Citation

UNAC tetraloops: to what extent do they mimic GNRA tetraloops?
Zhao, Q., Huang, H., Nagaswamy, U., Xia, Y., Gao, X., Fox, G.E.
Biopolymers (2012), 97, 617-628, PubMed 22605553 , DOI 10.1002/bip.22049 , Abstract

Related entities 1. UNAC Tetraloops, : 1 : 3 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_18079_4a4r.nef
Input source #2: Coordindates	4a4r.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:1:GMP:O3'	1:2:G:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	GMP	GUANOSINE	Assigned chemical shifts, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20--
XGACCCGGCUAACGCUGGGUCC
||||||||||||||||||||||
XGACCCGGCUAACGCUGGGUCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	22	0	0	100.0

Content subtype: combined_18079_4a4r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	90		100.0 (chain: A, length: 22)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	198 (198)	.	100.0 (chain: A, length: 22)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
1	GMP

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	187	88	47.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	56	44.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	32	52.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	10	76.9

Covalent bonds

Saveframe: assembly
- Status: OK

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of restraints: 198
- Total number of restraints per polymer type: 198
- Weight of restraints: 1.0 (198)
- Potential type of restraints: square-well-parabolic (198)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords evolution, GNRA tetraloop, NMR, RNA, structure, UMAC tetraloop

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Found 1 Document (0.428 seconds)

BMRB: 18079

Sample

Related entities 1. UNAC Tetraloops, : 1 : 3 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail