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- PDB-1c4l: SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR -

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Basic information

Entry
Database: PDB / ID: 1c4l
TitleSOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR
Components
  • RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')
  • RNA (5'-R(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3')
KeywordsRNA / C-U base pair
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsTanaka, Y. / Kojima, C. / Yamazaki, T. / Kodama, T.S. / Yasuno, K. / Miyashita, S. / Ono, A.M. / Ono, A.S. / Kainosho, M. / Kyogoku, Y.
Citation
Journal: Biochemistry / Year: 2000
Title: Solution structure of an RNA duplex including a C-U base pair.
Authors: Tanaka, Y. / Kojima, C. / Yamazaki, T. / Kodama, T.S. / Yasuno, K. / Miyashita, S. / Ono, A. / Ono, A. / Kainosho, M. / Kyogoku, Y.
#1: Journal: Nucleic Acids Symp.Ser. / Year: 1997
Title: Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution
Authors: Tanaka, Y. / Kojima, C. / Yamazaki, T. / Kyogoku, Y. / Miyashita, S. / Ono, A.S. / Kainosho, M.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 1.4Dec 27, 2023Group: 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(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3')
B: RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,6952
Polymers5,6952
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 / 50SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS)
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2870.783 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS OLIGONUCLEOTIDE WAS CHEMICALLY SYNTHESIZED (PHOSPHORAMIDITE METHOD).
#2: RNA chain RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')


Mass: 2823.719 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS OLIGONUCLEOTIDE WAS CHEMICALLY SYNTHESIZED (PHOSPHORAMIDITE METHOD).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H NOESY
1222D 1H NOESY
2312D 1H NOESY
1422D PCOSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
1R[CGACUCAGG]_R[CCUG(15N4)CGUCG] (AMINO-NITROGEN OF CYTIDINE IS POINT-LABELED (> 95%))
2R[CGACUCAGG]_R[CCUG(15N4)CGUCG] (AMINO-NITROGEN OF CYTIDINE IS POINT-LABELED (> 95%))
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM(NACL) 7.0 1 atm300 K
250mM(NACL) 7.0 1 atm278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Bruker ARXBrukerARX5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.8.1BRUNGERrefinement
X-PLOR3.851BRUNGERstructure solution
X-PLOR3.8.1BRUNGERstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: DISTANCE CONSTRAINTS (NOE 433, HYDROGEN BOND (BASE-PAIR) 54), DIHEDRAL ANGLE CONSTRAINTS 45
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS)
Conformers calculated total number: 50 / Conformers submitted total number: 1

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