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Open data
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Basic information
Entry | Database: PDB / ID: 5imt | ||||||
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Title | Toxin receptor complex | ||||||
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![]() | TOXIN / Cytolysin | ||||||
Function / homology | ![]() negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / COPI-mediated anterograde transport / specific granule membrane ...negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule 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 / killing of cells of another organism / cell surface receptor signaling pathway / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / host cell plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Morton, C.J. / Lawrence, S.L. / Feil, S.C. / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.5 KB | Display | ![]() |
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PDB format | ![]() | 172 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.5 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5imwC ![]() 5imyC ![]() 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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1 | ![]()
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2 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 58935.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 8926.097 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 131 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/ZN.gif)
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![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PGE / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-ZN / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 67.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, zinc acetate, MES pH 6.0, copper sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→48.211 Å / Num. obs: 48423 / % possible obs: 99.6 % / Redundancy: 4 % / Net I/σ(I): 8.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S3R Resolution: 2.7001→48.211 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.92 Å2 / Biso mean: 40.9931 Å2 / Biso min: 16.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7001→48.211 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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