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- PDB-1f9l: Solution Structure of a 22-Nucleotide Hairpin Similar to the P5AB... -

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Entry
Database: PDB / ID: 1f9l
TitleSolution Structure of a 22-Nucleotide Hairpin Similar to the P5ABC Region of a Group I Ribozyme with Cobalt(III)hexammine Complexed to the GAAA Tetraloop
Components5'-R(*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*GP*CP*GP*CP*CP*)-3'
KeywordsRNA / GA mismatches / GAAA tetraloop / metal-ion binding / Cobalt(III)hexammine / hairpin / P5abc / group I intron
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics,
Model type detailsminimized average
AuthorsRudisser, S. / Tinoco Jr., I.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches.
Authors: Rudisser, S. / Tinoco Jr., I.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
SupersessionJul 28, 2009ID: 1EOR
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(*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*GP*CP*GP*CP*CP*)-3'


Theoretical massNumber of molelcules
Total (without water)7,1751
Polymers7,1751
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)1 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

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


Mass: 7175.371 Da / Num. of mol.: 1 / Fragment: P5ABC DOMAIN / Source method: obtained synthetically
Details: The RNA was enzymatically synthesized from a synthetic RNA template using T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop. In addition, the same constraints as for the 22-nucleotide hairpin ...Text: The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop. In addition, the same constraints as for the 22-nucleotide hairpin without Cobalt(III)hexammine were used. For RNA without Cobalt(III)Hexammine see entry 1EOR.

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Sample preparation

DetailsContents: 2.8 mM RNA, 10 mM sodium Phosphate, 200 mM NaCl, 0.1 mM EDTA pH 5.6, 3.4 mM Cobalt(III)Hexammine
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200 mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
Felix95MSIdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: restrained molecular dynamics, / Software ordinal: 1
Details: 356 NOE constraints, 16 sugar pucker constraints, 93 torsion angle constraints, 7 constraints between Cobalt(III)Hexammine and the GAAA tetraloop
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 1

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