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- PDB-1gwy: Crystal structure of the water-soluble state of the pore-forming ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gwy | ||||||
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Title | Crystal structure of the water-soluble state of the pore-forming cytolysin Sticholysin II | ||||||
![]() | STICHOLYSIN II | ||||||
![]() | CYTOLYSIN / PORE-FORMING TOXIN / HEMOLYSIS / CNIDOCYST | ||||||
Function / homology | ![]() nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mancheno, J.M. / Martin-Benito, J. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A. | ||||||
![]() | ![]() Title: Crystal and Electron Microscopy Structures of Sticholysin II Actinoporin Reveal Insights Into the Mechanism of Membrane Pore Formation Authors: Mancheno, J.M. / Martin-Benito, J. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.8 KB | Display | ![]() |
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PDB format | ![]() | 67 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o71C ![]() 1o72C ![]() 1iazS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 19302.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: May 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→32.27 Å / Num. obs: 31889 / % possible obs: 90.3 % / Observed criterion σ(I): 4 / Redundancy: 2.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.151 / % possible all: 90.3 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 32.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.086 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB CODE 1IAZ Resolution: 1.71→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 714940.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE ELECTRON DENSITY OF THE LOOP REGION COMPRISED BETWEEN RESIDUES 109-111 IS NOT WELL DEFINED, PRESUMABLY DUE TO A HIGH MOBILITY. THE OCUPATION AND B FACTORS OF THE TRP-110 SIDE CHAIN HAVE ...Details: THE ELECTRON DENSITY OF THE LOOP REGION COMPRISED BETWEEN RESIDUES 109-111 IS NOT WELL DEFINED, PRESUMABLY DUE TO A HIGH MOBILITY. THE OCUPATION AND B FACTORS OF THE TRP-110 SIDE CHAIN HAVE BEEN SET TO 0.00 AND 20.00, RESPECTIVELY, DUE TO THE POOR ELECTRON DENSITY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.759 Å2 / ksol: 0.428738 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.71→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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