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Yorodumi- PDB-7tdb: Crystal structure of the E. coli thiM riboswitch in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tdb | ||||||
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Title | Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions | ||||||
Components | thiM riboswitch RNA (83-MER) | ||||||
Keywords | RNA | ||||||
Function / homology | Chem-GMI / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Nuthanakanti, A. / Serganov, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tdb.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tdb.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/7tdb ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdb | HTTPS FTP |
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-Related structure data
Related structure data | 7td7C 7tdaC 7tdcC 2hojS 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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1 |
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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.) Escherichia coli (E. coli) | ||||||
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#2: Chemical | ChemComp-GMI / [ | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 46.74 % / Description: Rod-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop 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, 0.35 M NH4Cl, 10 mm MnCl2, and 30% (v/v) PEG2000 PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
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: 2.56→56.26 Å / Num. obs: 8128 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 83.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.56→2.67 Å / Redundancy: 14.9 % / Rmerge(I) obs: 3.817 / Num. unique obs: 966 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HOJ Resolution: 2.56→56.26 Å / SU ML: 0.583 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.47 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: 85.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→56.26 Å
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Refine LS restraints |
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LS refinement shell |
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