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- PDB-8gw2: Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gw2 | ||||||
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Title | Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant CP13-14 | ||||||
![]() | Heat-labile enterotoxin IIB, B chain | ||||||
![]() | TOXIN / E. coli / LTIIB / LT-IIb-B5 / adjuvant / Toll-like receptor binding / TLR2/TLR1 signaling pathway / GD1a binding / ganglioside binding / circular permutation | ||||||
Function / homology | perturbation of signal transduction in another organism / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / host cell membrane / toxin activity / extracellular region / Heat-labile enterotoxin IIB, B chain![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, S.H. / Yuan, Y.T. / Sue, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant (CP13-14) Authors: Hsu, S.H. / Yuan, Y.T. / Sue, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.3 KB | Display | ![]() |
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Full document | ![]() | 484.7 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qb5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11066.447 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M sodium citrate pH 6, 0.1 M MgCl2, 15% v/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→30 Å / Num. obs: 13510 / % possible obs: 98.48 % / Redundancy: 2.8 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.84 / Rrim(I) all: 0.14 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.71→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1289 / Rrim(I) all: 0.64 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QB5 Resolution: 2.71→25.78 Å / SU ML: 0.424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.2647 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→25.78 Å
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Refine LS restraints |
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LS refinement shell |
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