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Open data
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Basic information
Entry | Database: PDB / ID: 7wie | ||||||
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Title | The THF-II riboswitch bound to 7DG | ||||||
![]() | RNA (50-MER) | ||||||
![]() | RNA / Holo form | ||||||
Function / homology | 7-DEAZAGUANINE / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, L. / Fang, X. / Xiao, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into translation regulation by the THF-II riboswitch. Authors: Xu, L. / Xiao, Y. / Zhang, J. / Fang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 25.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 636.9 KB | Display | ![]() |
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Full document | ![]() | 637.4 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wi9SC ![]() 7wiaC ![]() 7wibC ![]() 7wifC ![]() 7wiiC 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
#1: RNA chain | Mass: 16287.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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#2: Chemical | ChemComp-7DG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100mM sodium citrate pH6.5, 1.5-2.5M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 5770 / % possible obs: 99.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 93.87 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.033 / Net I/σ(I): 11.7 / Num. measured all: 98354 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WI9 Resolution: 2.9→28.99 Å / SU ML: 0.1112 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2049 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.24 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→28.99 Å
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Refine LS restraints |
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LS refinement shell |
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