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Yorodumi- PDB-8boz: structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8boz | ||||||
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Title | structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS effector/immunity complex | ||||||
Components |
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Keywords | HYDROLASE / Phospholipase / immunity / adherent-invasive Escherichia coli (AIEC) / / protein secretion / Protein structure / AlphaFold2 | ||||||
Function / homology | Alpha/Beta hydrolase fold / Lipoprotein / Transmembrane protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Cambillau, C. / Roussel, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Activity and Crystal Structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS Effector/Immunity Complex Determined Using an AlphaFold2 Predicted Model. Authors: Le, T.T.H. / Kellenberger, C. / Boyer, M. / Santucci, P. / Flaugnatti, N. / Cascales, E. / Roussel, A. / Canaan, S. / Journet, L. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8boz.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8boz.ent.gz | 913.9 KB | Display | PDB format |
PDBx/mmJSON format | 8boz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8boz_validation.pdf.gz | 930.4 KB | Display | wwPDB validaton report |
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Full document | 8boz_full_validation.pdf.gz | 1016.1 KB | Display | |
Data in XML | 8boz_validation.xml.gz | 199 KB | Display | |
Data in CIF | 8boz_validation.cif.gz | 267.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8boz ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8boz | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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-Components
#1: Protein | Mass: 73992.266 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_17315 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G9AAY6 #2: Protein | Mass: 30662.744 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_17310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G9AAX8 #3: Chemical | ChemComp-CA / 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: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Tle3AIEC-Tli3AIEC crystals were obtained using a reservoir solution consisting of 20% v/v PEG 3350. Bis Tris propane pH 6.5, 0.2 M sodium acetate trihydrate after 44 days at 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48.75 Å / Num. obs: 78970 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.976 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.6→3.64 Å / Num. unique obs: 5814 / CC1/2: 0.383 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model Resolution: 3.6→48.74 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→48.74 Å
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Refine LS restraints |
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LS refinement shell |
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