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Yorodumi- PDB-6ii6: Crystal structure of the Makes Caterpillars Floppy (MCF)-Like eff... -
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-Basic information
Entry | Database: PDB / ID: 6ii6 | ||||||
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Title | Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio vulnificus MO6-24/O in complex with a human ADP-ribosylation factor 3 (ARF3) | ||||||
Components |
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Keywords | TOXIN/PROTEIN BINDING / MCF / ARF3 / MARTX TOXIN / EFFECTOR DOMAIN / TOXIN / TOXIN-HOST PROTEIN COMPLEX / TOXIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the Golgi membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / host cell cytosol / COPI-mediated anterograde transport / vesicle-mediated transport / intracellular protein transport / toxin activity / transferase activity / cysteine-type endopeptidase activity ...Synthesis of PIPs at the Golgi membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / host cell cytosol / COPI-mediated anterograde transport / vesicle-mediated transport / intracellular protein transport / toxin activity / transferase activity / cysteine-type endopeptidase activity / Golgi membrane / GTPase activity / GTP binding / host cell plasma membrane / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Lee, Y. / Kim, B.S. / Choi, S. / Lee, E.Y. / Park, S. / Hwang, J. / Kwon, Y. / Hyun, J. / Lee, C. / Eom, S.H. / Kim, M.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Makes caterpillars floppy-like effector-containing MARTX toxins require host ADP-ribosylation factor (ARF) proteins for systemic pathogenicity. Authors: Lee, Y. / Kim, B.S. / Choi, S. / Lee, E.Y. / Park, S. / Hwang, J. / Kwon, Y. / Hyun, J. / Lee, C. / Kim, J.F. / Eom, S.H. / Kim, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ii6.cif.gz | 224.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ii6.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ii6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6ii6 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6ii6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40821.262 Da / Num. of mol.: 2 / Fragment: MCF / Mutation: C3351S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: rtxA1 / Production host: Escherichia coli (E. coli) / References: UniProt: F1CLG9*PLUS #2: Protein | Mass: 19796.598 Da / Num. of mol.: 2 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61204 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | The sequence of MCF domain has been deposited to database with NCBI accession ID WP_015728045.1. ...The sequence of MCF domain has been deposited to database with NCBI accession ID WP_015728045.1. GAM at N-terminal were from expression tag. Residue C3351S represents mutation. | |
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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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.1 M Bis-Tris-HCl (pH 5.5), and 2% Tacsimate (pH 4.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 65267 / % possible obs: 98.1 % / Redundancy: 7 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 3375 / CC1/2: 0.889 / Rpim(I) all: 0.228 / Rrim(I) all: 0.612 |
-Processing
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Refinement | Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.845 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.946 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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