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- PDB-1i46: The solution structure of the mutant stem loop C 5'GUA3' triloop ... -

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Basic information

Entry
Database: PDB / ID: 1i46
TitleThe solution structure of the mutant stem loop C 5'GUA3' triloop of brome mosaic virus (+) strand RNA
Components5'-R(*GP*GP*UP*GP*CP*GP*UP*AP*GP*CP*AP*CP*C)-3'
KeywordsRNA / Triloop / Stem-Loop / Mutant / Replication / BMV
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsKim, C.-H. / Tinoco Jr., I.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter
Authors: Kim, C.-H. / Tinoco Jr., I.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: RNA motifs that determine specificity between a viral replicase and its promoter
Authors: Kao, C.C.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*GP*CP*GP*UP*AP*GP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,1731
Polymers4,1731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*CP*GP*UP*AP*GP*CP*AP*CP*C)-3'


Mass: 4172.541 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is a mutant triloop of which wild type sequence is naturally occured in BMV (+) strand RNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: The 5'GUA3' triloop mutant in 5 mM NaPhosphate buffer pH=6.5
Solvent system: 5mM Sodium Phosphate buffer pH 6.5, O.1 mM EDTA
Sample conditionsIonic strength: 5mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix95data analysis
X-PLOR3.1Brunger, A.structure solution
X-PLOR3.1Brunger, A.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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