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Open data
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Basic information
Entry | Database: PDB / ID: 5imy | ||||||
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Title | Trapped Toxin | ||||||
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![]() | toxin/toxin receptor / toxin-toxin receptor complex | ||||||
Function / homology | ![]() negative regulation of activation of membrane attack complex / complement binding / hemolysis in another organism / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / : ...negative regulation of activation of membrane attack complex / complement binding / hemolysis in another organism / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / : / host cell membrane / COPI-mediated anterograde transport / specific granule membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / blood coagulation / toxin activity / vesicle / membrane => GO:0016020 / cell surface receptor signaling pathway / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lawrence, S.L. / Morton, C.J. / Parker, M.W. | ||||||
![]() | ![]() Title: Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins. Authors: Lawrence, S.L. / Gorman, M.A. / Feil, S.C. / Mulhern, T.D. / Kuiper, M.J. / Ratner, A.J. / Tweten, R.K. / Morton, C.J. / Parker, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.6 KB | Display | ![]() |
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PDB format | ![]() | 339.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5imtC ![]() 5imwC ![]() 1s3rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 54213.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 9101.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Ammonium acetate, PEG 10000, Bis-Tris, Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.315 Å / Num. obs: 49244 / % possible obs: 99.9 % / Redundancy: 4.5 % / Net I/σ(I): 13.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S3R Resolution: 2.4→42.639 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.639 Å
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Refine LS restraints |
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LS refinement shell |
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