+Open data
-Basic information
Entry | Database: PDB / ID: 2m4q | ||||||
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Title | NMR structure of E. coli ribosomela decoding site with apramycin | ||||||
Components | RNA (27-MER) | ||||||
Keywords | RNA/antibiotic / RNA / antibiotic / decoding site / aminoglycoside / apramycin / RNA-antibiotic complex | ||||||
Function / homology | APRAMYCIN / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Puglisi, J.D. / Tsai, A. / Marshall, R. / Viani, E. | ||||||
Citation | Journal: Cell Rep / Year: 2013 Title: The impact of aminoglycosides on the dynamics of translation elongation. Authors: Tsai, A. / Uemura, S. / Johansson, M. / Puglisi, E.V. / Marshall, R.A. / Aitken, C.E. / Korlach, J. / Ehrenberg, M. / Puglisi, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m4q.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m4q.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 2m4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m4q_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 2m4q_full_validation.pdf.gz | 528.3 KB | Display | |
Data in XML | 2m4q_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2m4q_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/2m4q ftp://data.pdbj.org/pub/pdb/validation_reports/m4/2m4q | 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: 8656.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-AM2 / |
-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 | Ionic strength: .05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: X-PLOR / Developer: Brunger / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR constraints | NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 27 / NA epsilon-angle constraints total count: 19 / NA sugar pucker constraints total count: 26 / NOE constraints total: 626 / NOE intraresidue total count: 190 |
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 |
NMR ensemble rms | Distance rms dev: 0.025 Å |