[English] 日本語
Yorodumi- PDB-6h2e: Structure of the soluble AhlC of the tripartite alpha-pore formin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2e | ||||||
---|---|---|---|---|---|---|---|
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 / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Churchill-Angus, A.M. / Wilson, J.S. / Baker, P.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6h2e.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6h2e.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 6h2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2e_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6h2e_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 6h2e_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 6h2e_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2e ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29432.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: V469_08880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U6XZ15, UniProt: A0KLE2*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 62 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Magnesium chloride 0.1 M Tris pH 7 10 % (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2015 |
Radiation | Monochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→58.33 Å / Num. obs: 32942 / % possible obs: 99.8 % / Redundancy: 39.3 % / Biso Wilson estimate: 48.86 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 40.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 97395 / Rpim(I) all: 0.639 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.35→58.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.846 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.35→58.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|