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Yorodumi- PDB-6ii2: Crystal structure of alpha-beta hydrolase (ABH) and Makes Caterpi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ii2 | ||||||
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Title | Crystal structure of alpha-beta hydrolase (ABH) and Makes Caterpillars Floppy (MCF)-Like effectors of Vibrio vulnificus MO6-24/O | ||||||
Components | Putative RTX-toxin | ||||||
Keywords | TOXIN / ABH-MCF / MARTX TOXIN / EFFECTOR DOMAIN | ||||||
Function / homology | Function and homology information host cell cytosol / transferase activity / toxin activity / cysteine-type endopeptidase activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Lee, Y. / Kim, B.S. / Choi, S. / Lee, E.Y. / Park, S. / Hwang, J. / Kwon, Y. / Hyung, 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 | 6ii2.cif.gz | 442.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ii2.ent.gz | 361.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ii2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ii2_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 6ii2_full_validation.pdf.gz | 536.6 KB | Display | |
Data in XML | 6ii2_validation.xml.gz | 85.1 KB | Display | |
Data in CIF | 6ii2_validation.cif.gz | 113 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6ii2 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6ii2 | HTTPS FTP |
-Related structure data
Related structure data | 6ii0C 6ii6SC 6impSC 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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-Components
#1: Protein | Mass: 75158.172 Da / Num. of mol.: 4 / Fragment: ABH-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 Sequence details | The sequence has been deposited to database with the NCBI accession ID WP_015728045.1. N-termianl M ...The sequence has been deposited to database with the NCBI accession ID WP_015728045.1. N-termianl M is the initial Methionine. Residue C3351S represent 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: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 4000, 0.1M Tris-HCl (pH 8.5), 0.2M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 34303 / % possible obs: 89.9 % / Redundancy: 5.7 % / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 3.5→3.56 Å / Num. unique obs: 1698 / CC1/2: 0.562 / Rpim(I) all: 0.581 / Rrim(I) all: 1.509 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6II6 AND 6IMP Resolution: 3.5→49.6 Å / Cor.coef. Fo:Fc: 0.785 / Cor.coef. Fo:Fc free: 0.752 / SU B: 49.181 / SU ML: 0.746 / Cross valid method: THROUGHOUT / ESU R Free: 0.978 / 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: 59.345 Å2
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Refinement step | Cycle: 1 / Resolution: 3.5→49.6 Å
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Refine LS restraints |
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