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- PDB-7tdc: Crystal structure of the E. coli thiM riboswitch in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tdc | ||||||
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Title | Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions | ||||||
![]() | thiM riboswitch RNA (83-MER) | ||||||
![]() | RNA | ||||||
Function / homology | Chem-GMI / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nuthanakanti, A. / Serganov, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. Authors: Zeller, M.J. / Nuthanakanti, A. / Li, K. / Aube, J. / Serganov, A. / Weeks, K.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.3 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 703.3 KB | Display | ![]() |
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Full document | ![]() | 708.4 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7td7C ![]() 7tdaC ![]() 7tdbC ![]() 2hojS 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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Unit cell |
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Components
#1: RNA chain | Mass: 26860.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-GMI / [ | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.75 mM TPPc. Reservoir solution was 50 mM sodium ...Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.75 mM TPPc. Reservoir solution was 50 mM sodium cacodylate, pH 6.0, 0.3 M NH4Cl, 10 mm CaCl2, and 30% (v/v) PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→56.3 Å / Num. obs: 9133 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 84.79 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 12.9 % / Rmerge(I) obs: 3.73 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1026 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HOJ Resolution: 2.46→56.3 Å / SU ML: 0.521 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.444 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→56.3 Å
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Refine LS restraints |
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LS refinement shell |
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