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- PDB-3d2x: Structure of the thiamine pyrophosphate-specific riboswitch bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d2x | ||||||
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Title | Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate | ||||||
![]() | TPP-specific riboswitch | ||||||
![]() | RNA / riboswitch / thiamine pyrophosphate / oxythiamine pyrophosphate / antibiotic / drugs / complex | ||||||
Function / homology | Chem-D2X / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thore, S. / Frick, C. / Ban, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.3 KB | Display | ![]() |
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PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 861.5 KB | Display | ![]() |
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Full document | ![]() | 870.3 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d2gC ![]() 3d2vC ![]() 2ckyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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.) ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 12-18% 1,6-hexanediol, 0.5mM spermine, 10mM magnesium sulfate, 40mM 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: ![]() ![]() ![]() |
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: 2.5→15 Å / Num. all: 16736 / Num. obs: 16268 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.85 / Num. unique all: 934 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2cky Resolution: 2.5→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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