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Basic information

Entry
Database: PDB / ID: 1i9k
TitleTHE RNA I-MOTIF
Components5'-R(*UP*CP*CP*CP*CP*C)-3'
KeywordsRNA / i-motif
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / NMR-based simulated annealing
AuthorsSnoussi, K. / Nonin-Lecomte, S. / Lerou, J.L.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The RNA i-motif.
Authors: Snoussi, K. / Nonin-Lecomte, S. / Leroy, J.L.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*UP*CP*CP*CP*CP*C)-3'
B: 5'-R(*UP*CP*CP*CP*CP*C)-3'
C: 5'-R(*UP*CP*CP*CP*CP*C)-3'
D: 5'-R(*UP*CP*CP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,1484
Polymers7,1484
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 / 50structures with the least restraint violations
Representative

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Components

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


Mass: 1787.117 Da / Num. of mol.: 4 / 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
121DQF-COSY
131TOCSY
14131P-1H HETERO-TOCSY
15113C-1H HSQC

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Sample preparation

DetailsContents: 9.8 mM of unlabeled DNA
Sample conditionsIonic strength: sodium counterion / pH: 4.3 / Pressure: ambient / Temperature: 270 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.refinement
Felix98processing
VNMR6.2collection
MOLMOL2.4data analysis
Curvesdata analysis
RefinementMethod: NMR-based simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 1

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