+Open data
-Basic information
Entry | Database: PDB / ID: 4tsl | ||||||
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Title | Crystal structure of FraC with POC bound (crystal form I) | ||||||
Components | Fragaceatoxin C | ||||||
Keywords | TOXIN / actinoporin / pore-forming toxin / Membrane lipids / Phosphocholine / Lipid-protein interaction | ||||||
Function / homology | Function and homology information nematocyst / cytolysis in another organism / pore complex assembly / 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 | Actinia fragacea (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Caaveiro, J.M.M. / Tanaka, K. / Tsumoto, K. | ||||||
Citation | Journal: Nat Commun / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tsl.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tsl.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 4tsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/4tsl ftp://data.pdbj.org/pub/pdb/validation_reports/ts/4tsl | HTTPS FTP |
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-Related structure data
Related structure data | 3vwiSC 3w9pC 4tsnC 4tsoC 4tspC 4tsqC 4tsyC 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 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.) Actinia fragacea (sea anemone) / Plasmid: pGEM-T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9W5G6 |
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-Non-polymers , 6 types, 376 molecules
#2: Chemical | ChemComp-PC / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-ACT / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM POC, 3 mM DDM, 200 mM Li2SO4, 100 mM ammonium formate, 24% PEG 8000, 100 sodium acetate PH range: 4.1 - 4.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32.37 Å / Num. obs: 62950 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 14.34 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VWI Resolution: 1.6→32.37 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.246 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / 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: 18.817 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→32.37 Å
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Refine LS restraints |
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