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- PDB-7tzr: Crystal structure of the E. coli thiM riboswitch bound to N-methy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tzr | ||||||
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Title | Crystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16) | ||||||
![]() | RNA (80-MER) | ||||||
![]() | RNA / thiM TPP riboswitch | ||||||
Function / homology | : / N-methyl-1-(quinoxalin-6-yl)methanamine / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nuthanakanti, A. / Serganov, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.2 KB | Display | ![]() |
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PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.6 KB | Display | ![]() |
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Full document | ![]() | 775.7 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tzsC ![]() 7tztC ![]() 7tzuC ![]() 2gdiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() |
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-Non-polymers , 5 types, 39 molecules ![](data/chem/img/KWU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % / Description: shapeless rod cluster |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: TPP riboswitch RNA (0.2 mM) and 16 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 3 (compound 16) mM MgCl2. Reservoir solution containing 0.1 M sodium acetate ...Details: TPP riboswitch RNA (0.2 mM) and 16 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 3 (compound 16) 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9252 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 11400 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 42.65 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.101 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1061 / CC1/2: 0.656 / Rpim(I) all: 0.407 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GDI Resolution: 2.7→29.05 Å / SU ML: 0.4157 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9874 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: 43.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.05 Å
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Refine LS restraints |
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LS refinement shell |
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