+Open data
-Basic information
Entry | Database: PDB / ID: 5imt | ||||||
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Title | Toxin receptor complex | ||||||
Components |
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Keywords | TOXIN / Cytolysin | ||||||
Function / homology | Function and homology information 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 | Streptococcus intermedius (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7001 Å | ||||||
Authors | Morton, C.J. / Lawrence, S.L. / Feil, S.C. / Parker, M.W. | ||||||
Citation | Journal: Structure / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5imt.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5imt.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 5imt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5imt ftp://data.pdbj.org/pub/pdb/validation_reports/im/5imt | HTTPS FTP |
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-Related structure data
Related structure data | 5imwC 5imyC 1s3rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Streptococcus intermedius (bacteria) / Gene: ily / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCB8 |
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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.) Homo sapiens (human) / Gene: CD59, MIC11, MIN1, MIN2, MIN3, MSK21 / Production host: Escherichia coli (E. coli) / References: UniProt: P13987 |
-Non-polymers , 5 types, 131 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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