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Yorodumi- PDB-7td7: Crystal structure of an E. coli thiM riboswitch bound to thiamine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7td7 | ||||||
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Title | Crystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions | ||||||
Components | thiM riboswitch RNA (78-MER) | ||||||
Keywords | RNA | ||||||
Function / homology | : / Chem-VIB / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 7td7.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7td7.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 7td7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7td7_validation.pdf.gz | 605.1 KB | Display | wwPDB validaton report |
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Full document | 7td7_full_validation.pdf.gz | 607.1 KB | Display | |
Data in XML | 7td7_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 7td7_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/7td7 ftp://data.pdbj.org/pub/pdb/validation_reports/td/7td7 | HTTPS FTP |
-Related structure data
Related structure data | 7tdaC 7tdbC 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: 26798.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) | ||||
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#2: Chemical | ChemComp-MN / | ||||
#3: Chemical | #4: Chemical | ChemComp-VIB / | 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: 2.08 Å3/Da / Density % sol: 40.87 % / Description: Rod-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 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 1.0 mM of thiamine. the reservoir solution was 50 mM Bis- ...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 1.0 mM of thiamine. the reservoir solution was 50 mM Bis-Tris HCl, pH 6.5, 0.5 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 4766 / % possible obs: 98.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 89.44 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.043 / Net I/σ(I): 47.6 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 445 / CC1/2: 0.933 / Rpim(I) all: 0.237 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HOJ Resolution: 2.95→29.3 Å / SU ML: 0.3703 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 41.5488 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: 110 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→29.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.6305134248 Å / Origin y: 19.5574279931 Å / Origin z: -5.61707477954 Å
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Refinement TLS group | Selection details: all |