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Open data
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Basic information
Entry | Database: PDB / ID: 7wif | ||||||
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Title | The THF-II riboswitch bound to H4B | ||||||
![]() | RNA (50-MER) | ||||||
![]() | RNA / Holo form | ||||||
Function / homology | 5,6,7,8-TETRAHYDROBIOPTERIN / 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 | ![]() | 47 KB | Display | ![]() |
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PDB format | ![]() | 26.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 650.1 KB | Display | ![]() |
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Full document | ![]() | 650.5 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wi9SC ![]() 7wiaC ![]() 7wibC ![]() 7wieC ![]() 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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1 |
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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-H4B / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.06 % |
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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: Jul 22, 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: 2.85→30 Å / Num. obs: 5787 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 80.59 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.035 / Net I/σ(I): 11.8 / Num. measured all: 85703 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WI9 Resolution: 2.86→28.68 Å / SU ML: 0.2921 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6659 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: 86.64 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→28.68 Å
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Refine LS restraints |
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LS refinement shell |
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