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- PDB-2kpc: Structure determination of the top-loop of the conserved 3 termin... -

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Basic information

Entry
Database: PDB / ID: 2kpc
TitleStructure determination of the top-loop of the conserved 3 terminal secondary structure in the genome of YFV
ComponentsRNA (5'-R(*UP*GP*AP*GP*CP*AP*CP*AP*GP*UP*UP*UP*GP*CP*UP*CP*A)-3')
KeywordsRNA / yellow fever virus / 3'-terminal loop / genome
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLescrinier, E. / Dyubankova, N. / Nauwelaerts, K. / Jones, R. / Herdewijn, P.
CitationJournal: Chembiochem / Year: 2010
Title: Structure Determination of the Top-Loop of the Conserved 3'-Terminal Secondary Structure in the Genome of Flaviviruses.
Authors: Lescrinier, E. / Dyubankova, N. / Nauwelaerts, K. / Jones, R. / Herdewijn, P.
History
DepositionOct 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: RNA (5'-R(*UP*GP*AP*GP*CP*AP*CP*AP*GP*UP*UP*UP*GP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,4041
Polymers5,4041
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)10 / 10all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

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


Mass: 5404.245 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
1122D 1H-13C HSQC
1222D DQF-COSY
1322D 1H-1H NOESY
1422D 1H-1H TOCSY
2522D 1H-1H NOESY
2612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM RNA, 90% H2O/10% D2O90% H2O/10% D2O
21-2 mM RNA, 100% D2O100% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMRNA1-21
mMRNA1-22
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 295 K
27ambient 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, C.D. et al.refinement
CARAKeller, R. et al.data analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: in water box
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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