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- PDB-8h2r: 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: 8h2r | ||||||
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Title | Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant CP52-53 | ||||||
![]() | 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 CP52-53 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 | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.6 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 29.1 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: 11066.451 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M sodium citrate pH 5, 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 MX-300 / Detector: CCD / Date: May 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 7547 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.82 Å2 / CC1/2: 0.87 / Rrim(I) all: 0.14 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7546 / Rrim(I) all: 0.63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QB5 Resolution: 2.9→26.8 Å / SU ML: 0.4918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.4411 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: 47.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→26.8 Å
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Refine LS restraints |
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LS refinement shell |
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