+Open data
-Basic information
Entry | Database: PDB / ID: 7a90 | ||||||
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Title | WT STING in complex with 3',3'-c-di[2'FdAM(PS)] | ||||||
Components | Stimulator of interferon protein | ||||||
Keywords | PROTEIN BINDING / Innate immune system / cyclic dinucleotides | ||||||
Function / homology | Function and homology information 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of type I interferon production / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / monoatomic ion transmembrane transport ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of type I interferon production / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / monoatomic ion transmembrane transport / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.185 Å | ||||||
Authors | Boura, E. / Smola, M. | ||||||
Citation | Journal: To Be Published Title: WT STING in complex with 3',3'-c-di[2'FdAM(PS)] Authors: Boura, E. / Smola, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a90.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a90.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 7a90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a90_validation.pdf.gz | 827.7 KB | Display | wwPDB validaton report |
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Full document | 7a90_full_validation.pdf.gz | 830.1 KB | Display | |
Data in XML | 7a90_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 7a90_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/7a90 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a90 | HTTPS FTP |
-Related structure data
Related structure data | 4ksyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23189.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3XZB7 |
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#2: Chemical | ChemComp-R4T / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M tri-Potassium Citrate monohydrate, 20% (w/v) PEG 3350, 0.1 M Natrium Citrate, 50 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.185→35.042 Å / Num. obs: 4032 / % possible obs: 99.8 % / Redundancy: 11.6 % / CC1/2: 0.967 / Net I/σ(I): 5.84 |
Reflection shell | Resolution: 3.185→3.299 Å / Mean I/σ(I) obs: 1.91 / Num. unique obs: 390 / CC1/2: 0.678 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KSY Resolution: 3.185→35.04 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.31 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 95.81 Å2 / Biso mean: 33.5966 Å2 / Biso min: 13.81 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.185→35.04 Å
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LS refinement shell | Resolution: 3.185→3.299 Å / Rfactor Rfree error: 0
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