[English] 日本語
Yorodumi- PDB-3d2x: Structure of the thiamine pyrophosphate-specific riboswitch bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d2x | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate | ||||||
Components | TPP-specific riboswitch | ||||||
Keywords | RNA / riboswitch / thiamine pyrophosphate / oxythiamine pyrophosphate / antibiotic / drugs / complex | ||||||
Function / homology | Chem-D2X / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3d2x.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3d2x.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d2x_validation.pdf.gz | 861.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3d2x_full_validation.pdf.gz | 870.3 KB | Display | |
Data in XML | 3d2x_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3d2x_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2x ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2x | HTTPS FTP |
-Related structure data
Related structure data | 3d2gC 3d2vC 2ckyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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) / Plasmid details: In vitro transcription / Production host: cell-free synthesis (others) #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2cky Resolution: 2.5→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
|