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- PDB-2fdt: Solution structure of a conserved RNA hairpin of eel LINE UnaL2 -

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Basic information

Entry
Database: PDB / ID: 2fdt
TitleSolution structure of a conserved RNA hairpin of eel LINE UnaL2
Components36-mer
KeywordsRNA / RDC / LINE / retrotransposition / RNA hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsNomura, Y. / Baba, S. / Nakazato, S. / Sakamoto, T. / Kajikawa, M. / Okada, N. / Kawai, G.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Authors: Nomura, Y. / Kajikawa, M. / Baba, S. / Nakazato, S. / Imai, T. / Sakamoto, T. / Okada, N. / Kawai, G.
History
DepositionDec 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 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: 36-mer


Theoretical massNumber of molelcules
Total (without water)11,5601
Polymers11,5601
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)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 36-mer


Mass: 11559.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: LINE36 were synthesized enzymatically by in vitro transcription with AmpliScribe T7 or T7 Flash transcription kits (Epicentre Technologies Co.) using by 13C- and 15N-labeled NTPs (Taiyo Nippon sanso).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY, 2D TOCSY
1222D NOESY, 2D TOCSY, DQF-COSY, HP-COSY
1332D HNN-COSY, 2D HSQC
144HCP, HALF FILTERED NOESY, 2D HSQC, 2D TROSY
1552D HNN-COSY, 2D HSQC
166HCP, HALF FILTERED NOESY, 2D HSQC, 2D TROSY
1772D HSQC, 2D TROSY
1882D HSQC, 2D TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9mM RNA; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 95% H2O, 5% D2O95% H2O/5% D2O
20.9mM RNA; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 100% D2O100% D2O
30.3mM RNA U-15N, 13C-GUANOSINE, CYTIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 95% H2O, 5% D2O95% H2O/5% D2O
40.3mM RNA U-15N, 13C-GUANOSINE, CYTIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 100% D2O100% D2O
50.9mM RNA U-15N, 13C-ADENOSINE, URIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 95% H2O, 5% D2O95% H2O/5% D2O
60.9mM RNA U-15N, 13C-ADENOSINE, URIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 100% D2O100% D2O
70.3mM RNA U-15N, 13C-GUANOSINE, CYTIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 16mg/ml PF1 BACTERIAPHAGE; 100% D2O100% D2O
80.9mM RNA U-15N, 13C-ADENOSINE, URIDINE; 10mM PHOSPHATE BUFFER (pH 6.0); 50mM NACL; 16mg/ml PF1 BACTERIAPHAGE; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
Felix97data analysis
Discover97structure solution
XPLOR-NIH2.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A total of 404 NOE distance restraints including the seven restraints for the absence of NOE cross peaks, 182 dihedral restraints, 62 hydrogen bonding restraints, 11 planarity restraints and ...Details: A total of 404 NOE distance restraints including the seven restraints for the absence of NOE cross peaks, 182 dihedral restraints, 62 hydrogen bonding restraints, 11 planarity restraints and 144 chiral restraints were used.Furthermore, refinement structures using 75 RDC restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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