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Yorodumi- PDB-6h2d: Structure of the soluble AhlC of the tripartite alpha-pore formin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2d | ||||||
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Title | Structure of the soluble AhlC of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila. | ||||||
Components | AhlC | ||||||
Keywords | TOXIN / Tripartite pore-forming toxin | ||||||
Function / homology | membrane => GO:0016020 / membrane / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Churchill-Angus, A.M. / Wilson, J.S. / Baker, P.J. | ||||||
Funding support | United Kingdom, 1items
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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 | 6h2d.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2d.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2d ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2d | HTTPS FTP |
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-Related 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: 29432.096 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: SAMN05880569_102658 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1N6TH80, UniProt: A0KLE2*PLUS |
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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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Sodium chloride 0.1 M Tris pH 8 20 % (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014 | |||||||||||||||
Radiation | Monochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.62→46.74 Å / Num. obs: 31150 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.858 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.058 / Net I/σ(I): 11 | |||||||||||||||
Reflection shell | Resolution: 2.62→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2309 / Rpim(I) all: 0.509 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet AhlC Resolution: 2.62→46.74 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.86 / SU B: 15.437 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.789 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.841 Å2
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Refinement step | Cycle: 1 / Resolution: 2.62→46.74 Å
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Refine LS restraints |
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