+Open data
-Basic information
Entry | Database: PDB / ID: 8xzk | ||||||
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Title | Crystal structure of folE riboswitch | ||||||
Components | RNA (53-MER) | ||||||
Keywords | RNA / riboswitch | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | unidentified eubacterium clone A70 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Li, C.Y. / Ren, A.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Structure-based characterization and compound identification of the wild-type THF class-II riboswitch. Authors: Li, C. / Xu, X. / Geng, Z. / Zheng, L. / Song, Q. / Shen, X. / Wu, J. / Zhao, J. / Li, H. / He, M. / Tai, X. / Zhang, L. / Ma, J. / Dong, Y. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xzk.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xzk.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 8xzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/8xzk ftp://data.pdbj.org/pub/pdb/validation_reports/xz/8xzk | HTTPS FTP |
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-Related structure data
Related structure data | 8xzeC 8xzlC 8xzmC 8xznC 8xzoC 8xzpC 8xzqC 8xzrC 8xzwC 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: 17094.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified eubacterium clone A70 (bacteria) Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v MPD, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→41.37 Å / Num. obs: 4721 / % possible obs: 89 % / Redundancy: 11.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 1.02 / Net I/σ(I): 16.9 / Num. measured all: 55367 |
Reflection shell | Resolution: 2.58→2.72 Å / % possible obs: 25.4 % / Redundancy: 10.1 % / Rmerge(I) obs: 1.53 / Num. measured all: 1902 / Num. unique obs: 188 / CC1/2: 0.766 / Rpim(I) all: 0.477 / Rrim(I) all: 1.607 / Χ2: 0.72 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→36.55 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→36.55 Å
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Refine LS restraints |
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LS refinement shell |
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