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Open data
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Basic information
Entry | Database: PDB / ID: 2g1w | ||||||||||||||||||
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Title | NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1 | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / tmRNA / PK1 / pseudoknot / trans-translation | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / CNS dynamical annealing protocol for nucleic acids | ![]() Nonin-Lecomte, S. / Dardel, F. | ![]() ![]() Title: NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation. Authors: Nonin-Lecomte, S. / Felden, B. / Dardel, F. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.3 KB | Display | ![]() |
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PDB format | ![]() | 171.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 310.8 KB | Display | ![]() |
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Full document | ![]() | 377.6 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 7064.258 Da / Num. of mol.: 1 / Mutation: C1G, G13C / Source method: obtained synthetically Details: The sequence of this RNA naturally exists in Aquifex aeolicus (Bacteria) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: CNS dynamical annealing protocol for nucleic acids / Software ordinal: 1 Details: A- dynamical annealing protocol: 1. TAMD 30 ps at 20000K 2. first cooling stage TAMD 40ps 3. second slow cooling annealing stage, restrained molecular dynamics 35ps. 4. 10 cycles of energy ...Details: A- dynamical annealing protocol: 1. TAMD 30 ps at 20000K 2. first cooling stage TAMD 40ps 3. second slow cooling annealing stage, restrained molecular dynamics 35ps. 4. 10 cycles of energy minimization of 300 steps each. B- Energy minimization: 1-TAMD 10ps at 300K, 2- cooling over 9 ps and 10 Powell cycles of 800 steps each. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 15 |