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- PDB-8hy9: Bacterial STING from Riemerella anatipestifer in complex with 3'3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hy9 | |||||||||
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Title | Bacterial STING from Riemerella anatipestifer in complex with 3'3'-c-di-GMP | |||||||||
![]() | CD-NTase-associated protein 12 | |||||||||
![]() | SIGNALING PROTEIN / CD-NTase-associated protein 12 | |||||||||
Function / homology | Chem-C2E / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING. Authors: Hou, M.H. / Wang, Y.C. / Yang, C.S. / Liao, K.F. / Chang, J.W. / Shih, O. / Yeh, Y.Q. / Sriramoju, M.K. / Weng, T.W. / Jeng, U.S. / Hsu, S.D. / Chen, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.6 KB | Display | ![]() |
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PDB format | ![]() | 34.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 828.3 KB | Display | ![]() |
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Full document | ![]() | 830.6 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hwiC ![]() 8hwjC ![]() 8hy8C ![]() 8hynC ![]() 7ebdS 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: Protein | Mass: 18563.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: (1) The first four AA, SGGG, is a linker. (2) The fifth AA, PHE5, should be indexed as PHE158. Thank you very much! Source: (gene. exp.) ![]() Gene: KYF39_09390 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-C2E / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 0.2 M calcium chloride dihydrate, 40 % v/v PEG 4000 |
-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: Oct 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→30 Å / Num. obs: 24248 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.227 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 2302 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EBD Resolution: 1.462→22.805 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.272 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.462→22.805 Å
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Refine LS restraints |
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LS refinement shell |
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