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- PDB-8tqx: Crystal structure of the Zika virus stem-loop A (SLA) bottom stem -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tqx | ||||||
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Title | Crystal structure of the Zika virus stem-loop A (SLA) bottom stem | ||||||
![]() | Zika virus stem-loop A (SLA) bottom stem | ||||||
![]() | RNA / Zika virus / Flavivirus / RNA structure / stem-loop A | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tipo, J. / Gottipati, K. / Choi, K.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. Authors: Tipo, J. / Gottipati, K. / Choi, K.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.8 KB | Display | ![]() |
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PDB format | ![]() | 19.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396 KB | Display | ![]() |
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Full document | ![]() | 396 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tsvC 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: 6054.634 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: A GGGCCC linker sequence is used to connect the antiparallel strands of the bottom stem Source: (synth.) ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Bis-Tris propane, magnesium chloride (MgCl2), and polyethylene glycol (PEG) 3350 PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 7321 / % possible obs: 94.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 56.15 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 0.946 / Net I/σ(I): 23.22 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 314 / CC1/2: 0.724 / CC star: 0.916 / Rpim(I) all: 0.484 / Χ2: 1.085 / % possible all: 83.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→48.83 Å
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Refine LS restraints |
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LS refinement shell |
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