+Open data
-Basic information
Entry | Database: PDB / ID: 7wi9 | ||||||
---|---|---|---|---|---|---|---|
Title | The THF-II riboswitch bound to THF and soaking with SeUrea | ||||||
Components | RNA (50-MER) | ||||||
Keywords | RNA / Holo form | ||||||
Function / homology | selenourea / (6S)-5,6,7,8-TETRAHYDROFOLATE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.98 Å | ||||||
Authors | Xu, L. / Fang, X. / Xiao, Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structural insights into translation regulation by the THF-II riboswitch. Authors: Xu, L. / Xiao, Y. / Zhang, J. / Fang, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wi9.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wi9.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wi9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7wi9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7wi9_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 7wi9_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/7wi9 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wi9 | HTTPS FTP |
-Related structure data
Related structure data | 7wiaC 7wibC 7wieC 7wifC 7wiiC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 16287.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) Production host: in vitro transcription vector pT7-TP(deltai) (others) | ||
---|---|---|---|
#2: Chemical | ChemComp-THG / ( | ||
#3: Chemical | ChemComp-SEY / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 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: 2.98→50 Å / Num. obs: 9359 / % possible obs: 99.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 83.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.111 / Net I/σ(I): 13.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.98→48.96 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0199 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.26 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.98→48.96 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|