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- PDB-2mxj: Structural features of a 3' splice site influenza A: 11-nt hairpin -

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Basic information

Entry
Database: PDB / ID: 2mxj
TitleStructural features of a 3' splice site influenza A: 11-nt hairpin
ComponentsRNA_(11-MER)
KeywordsRNA / influenza A / segment 7 / splice site / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest NOE restraint violation energy, model1
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 / Source and taxonomy
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_(11-MER)


Theoretical massNumber of molelcules
Total (without water)3,5521
Polymers3,5521
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 / 20lowest NOE restraint violation energy
RepresentativeModel #1lowest noe restraint violation energy

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Components

#1: RNA chain RNA_(11-MER)


Mass: 3552.234 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
2112D 1H-1H NOESY
3212D 1H-1H NOESY
1322D 1H-1H NOESY
4422D 1H-1H NOESY
1522D 1H-1H TOCSY
4622D 1H-1H TOCSY
1722D 1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM RNA (11-MER), 95% H2O/5% D2O95% H2O/5% D2O
24.0 mM RNA (11-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMRNA (11-MER)-11
4.0 mMRNA (11-MER)-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1101.126ambient atm293.15 K
2101.126ambient atm275.15 K
3101.126ambient atm272.15 K
4101.126ambient atm271.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
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 noe restraint violation energy
NMR ensembleConformer selection criteria: lowest NOE restraint violation energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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