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- PDB-2mxl: Structural features of a 3' splice site in influenza A: 39-nt hairpin -

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Basic information

Entry
Database: PDB / ID: 2mxl
TitleStructural features of a 3' splice site in influenza A: 39-nt hairpin
ComponentsRNA (39-MER)
KeywordsRNA / influenza A / segment 7 / splice site
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsTurner, D.H. / Kennedy, S.D. / Chen, J.L.
CitationJournal: Biochemistry / Year: 2015
Title: Structural features of a 3' splice site in influenza a.
Authors: Chen, J.L. / Kennedy, S.D. / Turner, D.H.
History
DepositionJan 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (39-MER)


Theoretical massNumber of molelcules
Total (without water)12,6891
Polymers12,6891
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)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (39-MER)


Mass: 12688.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1.1 mM RNA (39-MER), 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.1 mM / Component: RNA (39-MER)-1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1101.126ambient 293.15 K
2101.126ambient 271.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber11Case, D.A. et al.refinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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