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- PDB-2gip: Solution structure of a portion of the 5'UTR of HspA mRNA from Br... -

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Basic information

Entry
Database: PDB / ID: 2gip
TitleSolution structure of a portion of the 5'UTR of HspA mRNA from Bradyrhizobium janponicum having deleted G83
Components28-MER
KeywordsRNA / A form RNA helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / NMR
AuthorsChowdhury, S. / Maris, C. / Allain, F.H. / Narberhaus, F.
CitationJournal: Embo J. / Year: 2006
Title: Molecular basis for temperature sensing by an RNA thermometer.
Authors: Chowdhury, S. / Maris, C. / Allain, F.H. / Narberhaus, F.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 28-MER


Theoretical massNumber of molelcules
Total (without water)8,9011
Polymers8,9011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: RNA chain 28-MER


Mass: 8901.255 Da / Num. of mol.: 1 / Mutation: deletion of G83 / Source method: obtained synthetically
Details: the sequence for this RNA naturally occurs in BRADYRHIZOBIUM JAPONICUM.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D-NOESY-13CHSQC
1212D-NOESY
1312D-HSQC
141TOCSY
151HCcHTOCSY

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Sample preparation

DetailsContents: RNA
Sample conditionsIonic strength: 30mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 303 K

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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 DRX AVANCEBrukerDRX AVANCE6001
Bruker DRX AVANCEBrukerDRX AVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
Amber7David Case et al.refinement
DYANAprocessing
RefinementMethod: NMR / Software ordinal: 1 / Details: 20 structures
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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