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Yorodumi- PDB-2rpt: Structure of the CC mismatch from the thymidylate synthase bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rpt | ||||||||||||||||||
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Title | Structure of the CC mismatch from the thymidylate synthase binding site 1 hairpin and analysis of its interaction with paromomycin | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / NMR spectroscopy / RNA structure / paromomycin / aminoglycoside-RNA interaction | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS | Authors | Tavares, T.J. / Johnson, P.E. | Citation | Journal: Rna / Year: 2009 | Title: Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin Authors: Tavares, T.J. / Beribisky, A.V. / Johnson, P.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rpt.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rpt.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/2rpt ftp://data.pdbj.org/pub/pdb/validation_reports/rp/2rpt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 6450.943 Da / Num. of mol.: 1 / Fragment: thymidylate synthase binding site 1 mRNA hairpin / Source method: obtained synthetically / Details: IN-VITRO TRANSCRIPTION USING T7 RNA POLYMERASE |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA other-angle constraints total count: 55 / NA sugar pucker constraints total count: 20 / NOE constraints total: 260 / NOE intraresidue total count: 108 / NOE medium range total count: 43 / NOE sequential total count: 109 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1 |