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- PDB-2f87: Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 2f87
TitleSolution structure of a GAAG tetraloop in SRP RNA from Pyrococcus furiosus
ComponentsSRP RNA
KeywordsRNA / SRP / GNRR
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsOkada, K. / Takahashi, M. / Sakamoto, T. / Nakamura, K. / Kanai, A. / Kawai, G
CitationJournal: Nucleosides Nucleotides Nucleic Acids / Year: 2006
Title: Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus
Authors: Okada, K. / Takahashi, M. / Sakamoto, T. / Kawai, G. / Nakamura, K. / Kanai, A.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SRP RNA


Theoretical massNumber of molelcules
Total (without water)3,9061
Polymers3,9061
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)13 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain SRP RNA


Mass: 3906.400 Da / Num. of mol.: 1 / Fragment: pfHE6-12 / Source method: obtained synthetically
Details: The RNA fragment, pfHE6-12 was chemically synthesized by a phosphoramidite method, using an automatic DNA/RNA synthesizer, Expedite model 8909 (PerSeptive Biosystems).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2.0mM RNA Buffer Na; 95% H2O, 5% D2O; 2.0mM RNA; 20mM Phosphate Buffer Na; 100% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionClassification
Discover97structure solution
XwinNMR2.6collection
Felix97data analysis
Discover97refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 179 restraints, 127 are NOE-derived distance constraints, 34 dihedral angle restraints, 18 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 13

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