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- PDB-1r4h: NMR Solution structure of the IIIc domain of GB Virus B IRES Element -

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Basic information

Entry
Database: PDB / ID: 1r4h
TitleNMR Solution structure of the IIIc domain of GB Virus B IRES Element
Components5'-R(*GP*GP*GP*CP*AP*AP*GP*CP*CP*C)-3'
KeywordsRNA / GB Virus B / IRES / HAIRPIN Loop
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing restrained molecular dynamics complete relaxation matrix
Model type detailsminimized average
AuthorsKaluarachchi, K. / Thiviyanathan, V. / Rijinbrand, R. / Lemon, S.M. / Gorenstein, D.G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites.
Authors: Rijnbrand, R. / Thiviyanathan, V. / Kaluarachchi, K. / Lemon, S.M. / Gorenstein, D.G.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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*GP*CP*AP*AP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,2151
Polymers3,2151
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 / 10structures with acceptable covalent geometry,structures with favorable non-bond energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3215.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The SEQUENCE OCCURS NATURALLY IN GB Virus B AND WAS SYNTHESIZED In vitro trancription using T7 RNA Polymerase.

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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
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 10 mM phosphate, 10 mM KCL, 0.05 mM EDTA pH 6.8, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM KCl / pH: 6.8 / Pressure: ambient / Temperature: 298 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
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGER, Arefinement
Felix97BIOSYMdata analysis
RefinementMethod: distance geometry simulated annealing restrained molecular dynamics complete relaxation matrix
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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