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Open data
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Basic information
Entry | Database: PDB / ID: 4tsp | ||||||
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Title | Crystal structure of FraC with DHPC bound (crystal form II) | ||||||
![]() | Fragaceatoxin C | ||||||
![]() | TOXIN / actinoporin pore-forming toxin / Membrane / lipids Phosphocholine / Lipid-protein interaction | ||||||
Function / homology | ![]() nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / lipid binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caaveiro, J.M.M. / Tanaka, K. / Tsumoto, K. | ||||||
![]() | ![]() Title: Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Gonzalez-Manas, J.M. / Tsumoto, K. #1: Journal: Toxicon / Year: 2009 Title: Purification, cloning and characterization of fragaceatoxin C, a novel actinoporin from the sea anemone Actinia fragacea Authors: Bellomio, A. / Morante, K. / Barlic, A. / Gutierrez-Aguirre, I. / Viguera, A.R. / Gonzalez-Manas, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | 129.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vwiSC ![]() 3w9pC ![]() 4tslC ![]() 4tsnC ![]() 4tsoC ![]() 4tsqC ![]() 4tsyC 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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19746.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 131 molecules ![](data/chem/img/HXG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HXG / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-PC / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 50 mM DHPC, 200 mM Li2SO4, 20% PEG 1000, 100 mM phosphate-citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35.93 Å / Num. obs: 22701 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 79.7 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3VWI Resolution: 2.15→35.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.347 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.266 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→35.93 Å
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Refine LS restraints |
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