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Yorodumi- PDB-7mwy: Structure of the drosophila STING cyclic dinucleotide binding domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mwy | ||||||
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Title | Structure of the drosophila STING cyclic dinucleotide binding domain | ||||||
Components | STING | ||||||
Keywords | IMMUNE SYSTEM / STING / cyclic dinucleotide receptor | ||||||
Biological species | Drosophila eugracilis (fry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 Å | ||||||
Authors | Slavik, K.M. / Ragucci, A.E. / Kranzusch, P.J. | ||||||
Citation | Journal: Nature / Year: 2021 Title: cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila. Authors: Slavik, K.M. / Morehouse, B.R. / Ragucci, A.E. / Zhou, W. / Ai, X. / Chen, Y. / Li, L. / Wei, Z. / Bahre, H. / Konig, M. / Seifert, R. / Lee, A.S.Y. / Cai, H. / Imler, J.L. / Kranzusch, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mwy.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mwy.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mwy_validation.pdf.gz | 425 KB | Display | wwPDB validaton report |
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Full document | 7mwy_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 7mwy_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7mwy_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/7mwy ftp://data.pdbj.org/pub/pdb/validation_reports/mw/7mwy | HTTPS FTP |
-Related 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: 40901.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila eugracilis (fry) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate, 0.1 M Tris-HCl, 22% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→44.91 Å / Num. obs: 54801 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.42 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3340 / CC1/2: 0.435 / Rpim(I) all: 0.656 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: SAD-phased model of the selenomethionine derivative Resolution: 1.84→44.89 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5355 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: 40.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→44.89 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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