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- PDB-2lpt: Molecular dynamics re-refinement of domain 5 of the Pylaiella lit... -

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Basic information

Entry
Database: PDB / ID: 2lpt
TitleMolecular dynamics re-refinement of domain 5 of the Pylaiella littoralis group II intron
ComponentsRNA_(34-MER)
KeywordsRNA / Tetraloop / Bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 3
AuthorsHenriksen, N.M. / Davis, D.R. / Cheatham III, T.E.
CitationJournal: Rna / Year: 2006
Title: Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA.
Authors: Seetharaman, M. / Eldho, N.V. / Padgett, R.A. / Dayie, K.T.
History
DepositionFeb 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 0THIS ENTRY 2LPT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2F88.MR) ...THIS ENTRY 2LPT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2F88.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 2F88: M.SEETHARAMAN,N.V.ELDHO,R.A.PADGETT,K.T.DAYIE

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Structure visualization

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Assembly

Deposited unit
A: RNA_(34-MER)


Theoretical massNumber of molelcules
Total (without water)11,0101
Polymers11,0101
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)5 / 5all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA_(34-MER)


Mass: 11009.607 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a Molecular Dynamics re-refinement of structures from the PDB: 2F88 ensemble using the NMR restraints. The re-refinement shows significant changes in the overall geometry.
NMR detailsText: AUTHOR USED THE MR DATA FROM ENTRY 2F88.

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Processing

NMR softwareName: Amber / Version: 11
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5

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