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Yorodumi- PDB-3d2v: Structure of the eukaryotic TPP-specific riboswitch bound to the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d2v | ||||||
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Title | Structure of the eukaryotic TPP-specific riboswitch bound to the antibacterial compound pyrithiamine pyrophosphate | ||||||
Components | TPP-specific riboswitch | ||||||
Keywords | RNA / riboswitch / antibiotic / thiamine pyrophosphate / pyrithiamine pyrophosphate / complex | ||||||
Function / homology | Chem-PYI / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thore, S. / Frick, C. / Ban, N. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch Authors: Thore, S. / Frick, C. / Ban, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d2v.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d2v.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3d2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2v ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2v | HTTPS FTP |
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-Related structure data
Related structure data | 3d2gC 3d2xC 2ckyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 24958.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: In vitro transcription / Production host: cell-free synthesis (others) #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 12-18% 1,6-hexanediol, 0.5 mM spermine, 10 mM magnesium sulfate, 40 mM sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 33481 / Num. obs: 33092 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 5.87 / Num. unique all: 2372 / % possible all: 92.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine) / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2cky Resolution: 2→15 Å / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.257 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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