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Open data
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Basic information
Entry | Database: PDB / ID: 8oik | ||||||
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Title | D-PHAT domain (NTD) of human SAMD4A | ||||||
![]() | Protein Smaug homolog 1 | ||||||
![]() | RNA BINDING PROTEIN / protein interaction domain / dimerization domain | ||||||
Function / homology | ![]() nuclear-transcribed mRNA poly(A) tail shortening / translation repressor activity / positive regulation of translation / P-body / fibrillar center / cell junction / mRNA binding / synapse / dendrite / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kubikova, J. / Jeske, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar. Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M. #1: ![]() Title: Structural basis for binding of Smaug to the GPCR Smoothened and to the germline inducer Oskar Authors: Kubikova, J. / Ubartaite, G. / Metz, J. / Jeske, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.5 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8oijC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20829.803 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / | #3: Chemical | #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: 3.2 Å3/Da / Density % sol: 61.61 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 5.6, 8% jeffamine M-600 pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2019 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.62→63.05 Å / Num. obs: 89788 / % possible obs: 95.2 % / Redundancy: 13.8 % / Biso Wilson estimate: 33.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.062 / Net I/σ(I): 19.2 | |||||||||
Reflection shell | Resolution: 1.62→1.7 Å / Num. unique obs: 4488 / CC1/2: 0.34 |
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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: 41.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→49.45 Å
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Refine LS restraints |
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LS refinement shell |
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