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- PDB-2jym: Solution structure of stem-loop alpha of the hepatitis B virus po... -

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Entry
Database: PDB / ID: 2jym
TitleSolution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element
ComponentsRNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3')
KeywordsRNA / hepatitis B virus / post-transcriptional regulatory element / stem-loop alpha / NMR solution structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, force field-based em
AuthorsOhlenschlager, O. / Gorlach, M. / Schwalbe, M.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element
Authors: Schwalbe, M. / Ohlenschlager, O. / Marchanka, A. / Ramachandran, R. / Hafner, S. / Heise, T. / Gorlach, M.
History
DepositionDec 14, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 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: RNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,1051
Polymers7,1051
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)15 / 100target function
RepresentativeModel #1closest to the average

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Components

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


Mass: 7105.267 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2212D 1H-13C HSQC
2322D 1H-13C HSQC
1412D 1H-1H NOESY
2523D 1H-13C NOESY
2623D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C; U-100% 15N] RNA, 10mM potassium phosphate, 40mM potassium chloride, 0. mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-100% 13C; U-100% 15N] RNA, 10mM potassium phosphate, 40mM potassium chloride, 0.2mM EDTA, 99% D2O99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNA[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphate1
40 mMpotassium chloride1
0.2 mMEDTA1
1 mMRNA[U-100% 13C; U-100% 15N]2
10 mMpotassium phosphate2
40 mMpotassium chloride2
0.2 mMEDTA2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1506.2ambient atm283 K
2506.2ambient atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
VNMRVarianprocessing
VNMRVariancollection
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichcollection
RefinementMethod: DGSA-distance geometry simulated annealing, force field-based em
Software ordinal: 1 / Details: structure calculation, energy minimisation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15

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