+Open data
-Basic information
Entry | Database: PDB / ID: 7wii | ||||||
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Title | The THF-II riboswitch bound to NPR | ||||||
Components | RNA (50-MER) | ||||||
Keywords | RNA / THF-II riboswitch / NPR | ||||||
Function / homology | Chem-NPR / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Xu, L. / Fang, X. / Xiao, Y. | ||||||
Funding support | China, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wii.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wii.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wii_validation.pdf.gz | 665.8 KB | Display | wwPDB validaton report |
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Full document | 7wii_full_validation.pdf.gz | 667.2 KB | Display | |
Data in XML | 7wii_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 7wii_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/7wii ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wii | HTTPS FTP |
-Related structure data
Related structure data | 7wi9SC 7wiaC 7wibC 7wieC 7wifC 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
#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) |
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#2: Chemical | ChemComp-NPR / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.54 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.75→50 Å / Num. obs: 6580 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 88.67 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.095 / Χ2: 0.033 / Net I/σ(I): 10 / Num. measured all: 111627 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WI9 Resolution: 2.75→33.3 Å / SU ML: 0.2973 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.4707 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: 98.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→33.3 Å
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Refine LS restraints |
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LS refinement shell |
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