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Open data
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Basic information
Entry | Database: PDB / ID: 8xzo | ||||||
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Title | Crystal structure of folE riboswitch with Guanine | ||||||
![]() | RNA (53-MER) | ||||||
![]() | RNA / riboswitch / Guanine | ||||||
Function / homology | GUANINE / SPERMINE / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, C.Y. / Ren, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.5 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8xzeC ![]() 8xzkC ![]() 8xzlC ![]() 8xzmC ![]() 8xznC ![]() 8xzpC ![]() 8xzqC ![]() 8xzrC ![]() 8xzwC 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: 17174.043 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-SPM / | ||||
#3: Chemical | ChemComp-GUN / | ||||
#4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.58 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 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: 1.26→37.82 Å / Num. obs: 34010 / % possible obs: 67.4 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Χ2: 0.75 / Net I/σ(I): 12.2 / Num. measured all: 367905 |
Reflection shell | Resolution: 1.26→1.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.603 / Num. unique obs: 1286 / CC1/2: 0.303 / Rpim(I) all: 0.79 / Rrim(I) all: 0.199 / Χ2: 0.64 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.97→26.23 Å
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Refine LS restraints |
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LS refinement shell |
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