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Yorodumi- PDB-6h2f: Structure of the pre-pore AhlB of the tripartite alpha-pore formi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2f | ||||||
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Title | Structure of the pre-pore AhlB of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila. | ||||||
Components | AhlB | ||||||
Keywords | TOXIN / Tripartite pore-forming toxin | ||||||
Function / homology | Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / membrane => GO:0016020 / PHOSPHATE ION / Alpha-helical pore-forming toxin family protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Aeromonas hydrophila AL09-71 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 | 6h2f.cif.gz | 600.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2f.ent.gz | 500.6 KB | Display | PDB format |
PDBx/mmJSON format | 6h2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2f_validation.pdf.gz | 516.8 KB | Display | wwPDB validaton report |
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Full document | 6h2f_full_validation.pdf.gz | 550.9 KB | Display | |
Data in XML | 6h2f_validation.xml.gz | 102.9 KB | Display | |
Data in CIF | 6h2f_validation.cif.gz | 142.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2f ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2f | HTTPS FTP |
-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: 38734.520 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila AL09-71 (bacteria) Gene: A9R12_16795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A081US78, UniProt: A0KLE1*PLUS #2: Chemical | ChemComp-PO4 / |
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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: 3.29 Å3/Da / Density % sol: 62.61 % / Description: Stacked plates |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M ammonium phosphate 0.1 M Tris pH 8.5 50 % (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2014 |
Radiation | Monochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→39.55 Å / Num. obs: 165574 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.122 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.55→2.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 29762 / Rrim(I) all: 0.751 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet AhlB Resolution: 2.55→39.55 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.054 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.287 / 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: 39.264 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→39.55 Å
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Refine LS restraints |
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