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- PDB-1bj2: RNA LOOP-LOOP COMPLEX: THE COLE1 INVERTED LOOP SEQUENCE, NMR, 8 S... -

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Basic information

Entry
Database: PDB / ID: 1bj2
TitleRNA LOOP-LOOP COMPLEX: THE COLE1 INVERTED LOOP SEQUENCE, NMR, 8 STRUCTURES
Components
  • RNA (5'-R(*GP*CP*AP*CP*CP*GP*AP*AP*CP*CP*AP*UP*CP*CP*GP*GP*UP*GP*C)-3')
  • RNA (5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*AP*UP*GP*GP*UP*UP*CP*GP*UP*UP*GP*CP*C)-3')
KeywordsRNA / COLE1 RNA / LOOP-LOOP COMPLEX / KISS COMPLEX / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE MOLECULAR DYNAMICS
AuthorsLee, A.J. / Crothers, D.M.
CitationJournal: Structure / Year: 1998
Title: The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence.
Authors: Lee, A.J. / Crothers, D.M.
History
DepositionJul 2, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: RNA (5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*AP*UP*GP*GP*UP*UP*CP*GP*UP*UP*GP*CP*C)-3')
B: RNA (5'-R(*GP*CP*AP*CP*CP*GP*AP*AP*CP*CP*AP*UP*CP*CP*GP*GP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,8132
Polymers12,8132
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)8 / 80NO EXPERIMENTAL DATA VIOLATIONS
RepresentativeModel #1

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Components

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


Mass: 6761.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE LOOP-LOOP COMPLEX HAS INVERTED LOOP SEQUENCE
#2: RNA chain RNA (5'-R(*GP*CP*AP*CP*CP*GP*AP*AP*CP*CP*AP*UP*CP*CP*GP*GP*UP*GP*C)-3')


Mass: 6051.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE LOOP-LOOP COMPLEX HAS INVERTED LOOP SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
13115N/14N SELECTED NOESY
14113C/12C SELECTED NOESY
151(H)CCH-COSY
161(H)CCH-COSY
17131P
181MQHCN
19113C-HMQC
110115N-HMQC
NMR detailsText: FOR REPRESENTATIVE MODEL, SEE 2BJ2. THE STRUCTURE WAS DETERMINED USING DOUBLE AND TRIPLE RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED RNA.

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 25 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
GE UNITYGEUNITY6002
GE OMEGAGEOMEGA6003

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: TORSION ANGLE MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO EXPERIMENTAL DATA VIOLATIONS
Conformers calculated total number: 80 / Conformers submitted total number: 8

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