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Yorodumi- PDB-6r1j: Structure of the soluble AhlC triple head mutant of the tripartit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r1j | ||||||
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Title | Structure of the soluble AhlC triple head mutant of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila. | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TOXIN / Tripartite pore-forming toxin | ||||||
Function / homology | membrane / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Aeromonas hydrophila J-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Churchill-Angus, A.M. / Wilson, J.S. / Baker, P.J. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Identification and structural analysis of the tripartite alpha-pore forming toxin of Aeromonas hydrophila. Authors: Wilson, J.S. / Churchill-Angus, A.M. / Davies, S.P. / Sedelnikova, S.E. / Tzokov, S.B. / Rafferty, J.B. / Bullough, P.A. / Bisson, C. / Baker, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r1j.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r1j.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 6r1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r1j_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 6r1j_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 6r1j_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6r1j_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/6r1j ftp://data.pdbj.org/pub/pdb/validation_reports/r1/6r1j | HTTPS FTP |
-Related structure data
Related structure data | 6grjC 6grkC 6h2dC 6h2eSC 6h2fC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29153.662 Da / Num. of mol.: 2 / Mutation: L156T, L160T, L161T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila J-1 (bacteria) / Gene: V469_08880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U6XZ15, UniProt: A0KLE2*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M imidazole pH 8.0, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 103 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→76.86 Å / Num. obs: 52765 / % possible obs: 100 % / Redundancy: 18.7 % / CC1/2: 0.997 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.9 Å / Num. unique obs: 2550 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H2E Resolution: 1.92→76.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.539 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.155 / 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: 46.904 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→76.68 Å
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Refine LS restraints |
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