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- PDB-1tut: J4/5 Loop from the Candida albicans and Candida dubliniensis Grou... -

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Basic information

Entry
Database: PDB / ID: 1tut
TitleJ4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns
Components
  • 5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3'
  • 5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3'
KeywordsRNA / internal loop / tandem mismatch / GU pairs / AA pairs
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsZnosko, B.M. / Kennedy, S.D. / Wille, P.C. / Krugh, T.R. / Turner, D.H.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns.
Authors: Znosko, B.M. / Kennedy, S.D. / Wille, P.C. / Krugh, T.R. / Turner, D.H.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3'
B: 5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,0532
Polymers7,0532
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)1 / 50closest to average
RepresentativeModel #1closest to the average

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Components

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


Mass: 3648.282 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3'


Mass: 3405.034 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 NOESY
2222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 90% H2O, 10% D2O90% H2O/10% D2O
2~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
180 mM NaCl, 3 mM cobalt hexamine 6.1 ambient 298 K
280 mM NaCl, 3 mM cobalt hexamine 6.1 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Variancollection
Felix2000Felixdata analysis
Discover95Insightstructure solution
Discover95Insightrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 217 NMR-derived interproton distance restraints (108 intranucleotide and 109 internucleotide). Hydrogn bond restraints were used for the six WC pairs ...Details: The structures are based on a total of 217 NMR-derived interproton distance restraints (108 intranucleotide and 109 internucleotide). Hydrogn bond restraints were used for the six WC pairs and for the G8-U14 wobble pair. On the basis of NMR data that is consistent with the formation of tandem sheared AA pairs, two artificial hydrogen bonding restraints were used between each sheared AA pair.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: closest to average / Conformers calculated total number: 50 / Conformers submitted total number: 1

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