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Yorodumi- PDB-2lpt: Molecular dynamics re-refinement of domain 5 of the Pylaiella lit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lpt | ||||||
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Title | Molecular dynamics re-refinement of domain 5 of the Pylaiella littoralis group II intron | ||||||
Components | RNA_(34-MER) | ||||||
Keywords | RNA / Tetraloop / Bulge | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | closest to the average, model 3 | ||||||
Authors | Henriksen, N.M. / Davis, D.R. / Cheatham III, T.E. | ||||||
Citation | Journal: 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 |
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Remark 0 | THIS 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 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lpt.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lpt.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 2lpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/2lpt ftp://data.pdbj.org/pub/pdb/validation_reports/lp/2lpt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 11009.607 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: 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. |
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NMR details | Text: AUTHOR USED THE MR DATA FROM ENTRY 2F88. |
-Processing
NMR software | Name: AMBER / Version: 11 Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman Classification: refinement |
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Refinement | Method: molecular dynamics / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 5 / Conformers submitted total number: 5 |