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Yorodumi- PDB-8hwi: Bacterial STING from Larkinella arboricola in complex with 3'3'-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hwi | |||||||||
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Title | Bacterial STING from Larkinella arboricola in complex with 3'3'-c-di-GMP | |||||||||
Components | CD-NTase-associated protein 12 | |||||||||
Keywords | SIGNALING PROTEIN / CD-NTase-associated protein 12 | |||||||||
Function / homology | Prokaryotic STING domain / Prokaryotic STING domain / CD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain / : / NAD+ glycohydrolase / nucleotide binding / Chem-C2E / CD-NTase-associated protein 12 Function and homology information | |||||||||
Biological species | Larkinella arboricola (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | |||||||||
Authors | Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Nat Commun / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hwi.cif.gz | 235.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hwi.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 8hwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/8hwi ftp://data.pdbj.org/pub/pdb/validation_reports/hw/8hwi | HTTPS FTP |
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-Related structure data
Related structure data | 8hwjC 8hy8C 8hy9C 8hynC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20933.891 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Larkinella arboricola (bacteria) / Gene: LX87_05200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A327WNX5, NAD+ glycohydrolase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Imidazole pH 7.5, 0.1 M Sodium chloride, 20% v/v Jeffamine ED-2001 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→30 Å / Num. obs: 30140 / % possible obs: 96.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 45.98 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.72→2.82 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.526 / Num. unique obs: 2870 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→29.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.487 Å2
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Refinement step | Cycle: 1 / Resolution: 2.73→29.31 Å
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