+Open data
-Basic information
Entry | Database: PDB / ID: 7ebl | ||||||
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Title | Bacterial STING in complex with c-di-GMP | ||||||
Components | STING | ||||||
Keywords | SIGNALING PROTEIN / second messenger / complex / cyclic dinucleotide / antiviral pathway | ||||||
Function / homology | Chem-C2E Function and homology information | ||||||
Biological species | Myroides sp. ZB35 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Crystal structure and functional implication of bacterial STING. Authors: Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, C.-J. / Chiu, Y.-F. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebl.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebl.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ebl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ebl_validation.pdf.gz | 834.8 KB | Display | wwPDB validaton report |
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Full document | 7ebl_full_validation.pdf.gz | 839.8 KB | Display | |
Data in XML | 7ebl_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 7ebl_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebl ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebl | HTTPS FTP |
-Related structure data
Related structure data | 7ebdSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.9995781002, -0.0166128385123, -0.0238250959639), (0.0200411056817, -0.988214815931, -0.151755829072), (-0.0210232177408, -0.152169284584, 0.98813082795)Vector: 0. ...NCS oper: (Code: given Matrix: (-0.9995781002, -0.0166128385123, -0.0238250959639), Vector: |
-Components
#1: Protein | Mass: 19183.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myroides sp. ZB35 (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #2: Chemical | ChemComp-C2E / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The sequence has been deposited to NCBI under accession number WP_071307203. | |
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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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium cacodylate trihydrate pH 6.5, 0.2M sodium acetate trihydrate, 15% w/v polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→30 Å / Num. obs: 17092 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.052 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.17→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1680 / CC1/2: 0.859 / Rpim(I) all: 0.215 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EBD Resolution: 2.17→24.18 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.0571 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: 34.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→24.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.15037369713 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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