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Open data
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Basic information
Entry | Database: PDB / ID: 3c0m | ||||||
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Title | Crystal structure of the proaerolysin mutant Y221G | ||||||
![]() | Aerolysin | ||||||
![]() | TOXIN / CYTOLYTIC TOXIN / PORE-FORMING TOXIN / Membrane / Secreted | ||||||
Function / homology | ![]() toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernot, L. / Schiltz, M. / Thurnheer, S. / Burr, S.E. / van der Goot, G. | ||||||
![]() | ![]() Title: Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Authors: Degiacomi, M.T. / Iacovache, I. / Pernot, L. / Chami, M. / Kudryashev, M. / Stahlberg, H. / van der Goot, F.G. / Dal Peraro, M. #1: ![]() Title: Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states. Authors: Parker, M.W. / Buckley, J.T. / Postma, J.P. / Tucker, A.D. / Leonard, K. / Pattus, F. / Tsernoglou, D. #2: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization of a proform of aerolysin, a hole-forming toxin from Aeromonas hydrophila. Authors: Tucker, A.D. / Parker, M.W. / Tsernoglou, D. / Buckley, J.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.2 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 459 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c0nC ![]() 3c0oC ![]() 1preS 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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Unit cell |
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Components
#1: Protein | Mass: 51874.332 Da / Num. of mol.: 2 / Mutation: Y221G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 9-11% PEG 4000, 100mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→44.58 Å / Num. all: 24769 / Num. obs: 24769 / % possible obs: 91.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.123 / Rsym value: 0.087 / Net I/σ(I): 10.39 |
Reflection shell | Resolution: 2.88→3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.24 / Num. unique all: 6253 / Rsym value: 0.363 / % possible all: 67.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PRE Resolution: 2.88→44.56 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.12 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.88→44.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.88→3.06 Å / Rfactor Rfree error: 0.022
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