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- PDB-1mfk: Structure of Prokaryotic SECIS mRNA Hairpin -

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Basic information

Entry
Database: PDB / ID: 1mfk
TitleStructure of Prokaryotic SECIS mRNA Hairpin
Components5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*AP*CP*CP*GP*CP*C)-3'
KeywordsRNA / RNA tetraloop / (A/U)GNN tetraloop family / SelB
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFourmy, D. / Guittet, E. / Yoshizawa, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of Prokaryotic SECIS mRNA Hairpin and its Interaction with Elongation Factor SELB
Authors: Fourmy, D. / Guittet, E. / Yoshizawa, S.
History
DepositionAug 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 22, 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: 5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*AP*CP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3861
Polymers7,3861
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 / 200structures with the lowest energy
Representative

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Components

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


Mass: 7386.423 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE is from ESCHERICHIA COLI. T7 RNA polymerase in vitro transcription.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SECIS RNA non-label; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
21mM SECIS RNA non-label; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
31mM SECIS RNA U-15N, 13C; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
41mM SECIS RNA U-15N, 13C; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
51mM SECIS RNA U-15N; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
61mM SECIS RNA U-15N; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.4ambient 275 K
26.4ambient 278 K
36.4ambient 288 K
46.4ambient 293 K
56.4ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
DiscoverMOLECULAR SIMULATIONS INC.structure solution
DiscoverMOLECULAR SIMULATIONS INC.refinement
AURELIAdata analysis
XwinNMRprocessing
Gifaprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 260 NOE-derived distance constraints, 72 dihedral angle restraints
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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