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Yorodumi- PDB-7tzs: Crystal structure of the E. coli thiM riboswitch in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tzs | ||||||
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Title | Crystal structure of the E. coli thiM riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17) | ||||||
Components | RNA (80-MER) | ||||||
Keywords | RNA / thiM TPP riboswitch | ||||||
Function / homology | : / 1-(quinoxalin-6-yl)methanamine / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 | 7tzs.cif.gz | 197.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tzs.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 7tzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tzs_validation.pdf.gz | 865.2 KB | Display | wwPDB validaton report |
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Full document | 7tzs_full_validation.pdf.gz | 848.8 KB | Display | |
Data in XML | 7tzs_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 7tzs_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tzs ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tzs | HTTPS FTP |
-Related structure data
Related structure data | 7tzrC 7tztC 7tzuC 2gdiS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: givenMatrix: (0.316775711666, 0.158978259818, -0.935082382148), (0.131815119195, -0.983665630576, -0.122583447393), (-0.939296504225, -0.084426536874, -0.332557118435)Vector: 25. ...NCS oper: (Code: given Matrix: (0.316775711666, 0.158978259818, -0.935082382148), Vector: |
-Components
-RNA chain , 1 types, 2 molecules XY
#1: RNA chain | Mass: 26042.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % / Description: shapeless rod-clusters |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: TPP riboswitch RNA (0.2 mM) 17 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 5 (compound 17) mM MgCl2. Reservoir solution containing 0.1 M sodium acetate (pH ...Details: TPP riboswitch RNA (0.2 mM) 17 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 5 (compound 17) mM MgCl2. Reservoir solution containing 0.1 M sodium acetate (pH 4.8), 0.35 M ammonium acetate, and 28% (v/v) PEG4000 PH range: 4.8-6.8 |
-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: 0.9184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→29.78 Å / Num. obs: 21835 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 42.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.069 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1447 / CC1/2: 0.765 / Rpim(I) all: 0.623 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDI Resolution: 2.21→29.78 Å / SU ML: 0.3111 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1287 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: 53.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→29.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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