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Open data
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Basic information
Entry | Database: PDB / ID: 8hzd | ||||||
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Title | A new fluorescent RNA aptamer bound with N618 | ||||||
![]() | (RNA (36-MER)) x 2 | ||||||
![]() | RNA / fluorescent RNA aptamer | ||||||
Function / homology | : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, Q.Q. / Ren, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift. Authors: Huang, K. / Song, Q. / Fang, M. / Yao, D. / Shen, X. / Xu, X. / Chen, X. / Zhu, L. / Yang, 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 | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.9 KB | Display | ![]() |
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Full document | ![]() | 801.9 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hzeSC ![]() 8hzfC ![]() 8hzjC ![]() 8hzkC ![]() 8hzlC ![]() 8hzmC 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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Unit cell |
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Components
#1: RNA chain | Mass: 11620.019 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: in vitro transcription vector pT7-TP(deltai) (others) | ||||||
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#2: RNA chain | Mass: 11699.999 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: in vitro transcription vector pT7-TP(deltai) (others) | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | Mass: 365.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H13F2N3O2 / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.05 M Magnesium Chloride, 0.1 M HEPES pH7.5, 30%(w/v) PEGmm550, 0.001 M GSH |
-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: Nov 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.102 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→38.86 Å / Num. obs: 14913 / % possible obs: 96.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.87→1.97 Å / Rmerge(I) obs: 0.648 / Num. unique obs: 3566 / CC1/2: 0.883 / Rpim(I) all: 0.279 / Rrim(I) all: 0.713 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8HZE Resolution: 1.87→28.16 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.5 / 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: 1.87→28.16 Å
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Refine LS restraints |
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LS refinement shell |
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