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Open data
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Basic information
Entry | Database: PDB / ID: 8hzm | ||||||
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Title | A new fluorescent RNA aptamer bound with N, manganese soak | ||||||
![]() | RNA (36-MER) | ||||||
![]() | RNA / Fluorescent RNA aptamer | ||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, K.Y. / 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 | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 39.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hzdC ![]() 8hzeSC ![]() 8hzfC ![]() 8hzjC ![]() 8hzkC ![]() 8hzlC 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
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 11274.813 Da / Num. of mol.: 2 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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-Non-polymers , 6 types, 64 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | Mass: 361.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N3O2 / Feature type: SUBJECT OF INVESTIGATION #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.71 % |
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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%polyethylene glycol monomethyl ether 550, 0.6% 1,6-diaminohexane |
-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: Apr 20, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 6395 / % possible obs: 97.1 % / Redundancy: 5.9 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.049 / Rrim(I) all: 0.126 / Χ2: 1.254 / Net I/σ(I): 4.5 / Num. measured all: 37919 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8HZE Resolution: 2.5→39.14 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.36 / 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: 2.5→39.14 Å
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Refine LS restraints |
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LS refinement shell |
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