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Yorodumi- PDB-8a2x: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a2x | ||||||||||||||||||||||||||||||
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Title | Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP(S)-2'F,2'dComponents | Stimulator of interferon protein | Keywords | ANTIVIRAL PROTEIN / sting / antiviral / activator | 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 / Resolution: 3 Å | Authors | Klima, M. / Smola, M. / Boura, E. | Funding support | 1items |
Citation | Journal: To Be Published | Title: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP(S)-2'F,2'd Authors: Klima, M. / Smola, M. / Boura, E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a2x.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a2x.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a2x_validation.pdf.gz | 888.2 KB | Display | wwPDB validaton report |
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Full document | 8a2x_full_validation.pdf.gz | 888.2 KB | Display | |
Data in XML | 8a2x_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 8a2x_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2x ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2x | HTTPS FTP |
-Related structure data
Related structure data | 4ksyS S: Starting model for refinement |
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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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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 BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7 |
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#2: Chemical | ChemComp-KZA / |
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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium acetate, 20% (w/v) PEG 3350 |
-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: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.25 Å / Num. obs: 4778 / % possible obs: 99.21 % / Redundancy: 11.6 % / Biso Wilson estimate: 62.71 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2494 / Rpim(I) all: 0.07549 / Rrim(I) all: 0.261 / Net I/σ(I): 9.86 |
Reflection shell | Resolution: 3→3.108 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.493 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 443 / CC1/2: 0.69 / CC star: 0.904 / Rpim(I) all: 0.4293 / Rrim(I) all: 1.555 / % possible all: 98.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ksy Resolution: 3→39.25 Å / SU ML: 0.3518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7232 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.25 Å
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Refine LS restraints |
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LS refinement shell |
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