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Yorodumi- PDB-7tzt: Crystal structure of the E. coli thiM riboswitch in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tzt | ||||||
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Title | Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37) | ||||||
Components | RNA (79-MER) | ||||||
Keywords | RNA / thiM TPP riboswitch | ||||||
Function / homology | 6-methylquinoxaline / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | ||||||
Authors | Nuthanakanti, A. / Serganov, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: SHAPE-enabled fragment-based ligand discovery for RNA. Authors: Zeller, M.J. / Favorov, O. / Li, K. / Nuthanakanti, A. / Hussein, D. / Michaud, A. / Lafontaine, D.A. / Busan, S. / Serganov, A. / Aube, J. / 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 | 7tzt.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tzt.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 7tzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tzt_validation.pdf.gz | 638.1 KB | Display | wwPDB validaton report |
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Full document | 7tzt_full_validation.pdf.gz | 640.5 KB | Display | |
Data in XML | 7tzt_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 7tzt_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tzt ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tzt | HTTPS FTP |
-Related structure data
Related structure data | 7tzrC 7tzsC 7tzuC 2hojS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-KXC / | 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: 2.06 Å3/Da / Density % sol: 40.36 % / Description: large trigonal shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: The 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 compound 38. Reservoir solution was 50 mM Bis- ...Details: The 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 compound 38. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.5 M ammonium chloride, 15 mm MnCl2, and 28% (v/v) PEG2000 PH range: 6.5-8.0 |
-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: 2.93→50 Å / Num. obs: 4715 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 97.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.044 / Net I/σ(I): 304.8 |
Reflection shell | Resolution: 2.93→2.98 Å / Redundancy: 10.6 % / Rmerge(I) obs: 3.612 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 238 / CC1/2: 0.637 / Rpim(I) all: 1.14 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HOJ Resolution: 2.96→47 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.9635 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: 115.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→47 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: -8.30212374089 Å / Origin y: 16.841211741 Å / Origin z: 5.43754207531 Å
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Refinement TLS group | Selection details: all |