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- PDB-2rlu: The Three Dimensional Structure of the Moorella thermoacetica Sel... -

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Entry
Database: PDB / ID: 2rlu
TitleThe Three Dimensional Structure of the Moorella thermoacetica Selenocysteine Insertion Sequence RNA Hairpin and its Interaction with the Elongation factor SelB
ComponentsRNA (5'-R(*GP*GP*UP*UP*GP*CP*GP*GP*GP*UP*CP*UP*CP*GP*CP*AP*AP*CP*C)-3')
KeywordsRNA / RNA structure / Selenocysteine / SelB / protein-RNA interactions
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsThree dimensional structure of the Selenocysteine Insertion Sequence from Moorella thermoacetica ...Three dimensional structure of the Selenocysteine Insertion Sequence from Moorella thermoacetica determined by NMR spectroscopy
AuthorsBeribisky, A.V. / Tavares, T.J. / Amborski, A.N. / Motamed, M. / Johnson, A.E. / Mark, T.L. / Johnson, P.E.
CitationJournal: Rna / Year: 2007
Title: The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB
Authors: Beribisky, A.V. / Tavares, T.J. / Amborski, A.N. / Motamed, M. / Johnson, A.E. / Mark, T.L. / Johnson, P.E.
History
DepositionAug 21, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2020Group: Data collection / Derived calculations / Structure summary
Category: ndb_struct_na_base_pair / pdbx_nmr_software ...ndb_struct_na_base_pair / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _pdbx_nmr_software.name / _struct_keywords.text
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0861
Polymers6,0861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the noe lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6085.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In-vitro transcription using T7 RNA polymerase.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Three dimensional structure of the Selenocysteine Insertion Sequence from Moorella thermoacetica determined by NMR spectroscopy
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H NOESY
2322D 1H-1H TOCSY
2442D 1H-13C HSQC
1532D 1H-15N HSQC
2643D 1H-13C NOESY
1733D 1H-15N NOESY
2843D (H)CCH-TOCSY
2943D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13-5mg SECIS-MT RNA, 90% H2O/10% D2O90% H2O/10% D2O
23-5mg SECIS-MT RNA, 100% D2O100% D2O
33-5mg [U-100% 13C; U-100% 15N] SECIS-MT RNA, 90% H2O/10% D2O90% H2O/10% D2O
43-5mg [U-100% 13C; U-100% 15N] SECIS-MT RNA, 100% D2O100% D2O
Sample conditions
Conditions-IDTemperature (K)
1278 K
2298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the noe lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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