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Yorodumi- PDB-2m39: The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m39 | ||||||||||||||||||||||
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Title | The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX | ||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / DUPLEX / (3' / 5')-RNA / 2'-O-(2-METHOXYETHYL) RIBOSE | Function / homology | RNA / RNA (> 10) | Function and homology information Biological species | Synthetic (others) | Method | SOLUTION NMR / simulated annealing, energy minimization | Model details | lowest energy, model7 | Authors | Plevnik, M. / Cevec, M. / Plavec, J. | Citation | Journal: Biochimie / Year: 2013 | Title: NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. Authors: Plevnik, M. / Cevec, M. / Plavec, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m39.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m39.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 2m39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m39_validation.pdf.gz | 340.6 KB | Display | wwPDB validaton report |
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Full document | 2m39_full_validation.pdf.gz | 543.8 KB | Display | |
Data in XML | 2m39_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2m39_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/2m39 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/2m39 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 4534.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY / Source: (synth.) Synthetic (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND HETERONUCLEAR TECHNIQUES. |
-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Varian Unity Inova / Manufacturer: Varian / Model: Unity Inova / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, energy minimization / Software ordinal: 1 Details: STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY ...Details: STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 3',5'-PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O2' OF EACH RIBOSE MODIFIED BY METHOXYETHYL. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 394 | ||||||||||||||||||||||||
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: 9 |