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Open data
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Basic information
Entry | Database: PDB / ID: 1olp | ||||||
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Title | Alpha Toxin from Clostridium Absonum | ||||||
![]() | ALPHA-TOXIN | ||||||
![]() | HYDROLASE / ZINC PHOSPHOLIPASE C / GAS GANGRENE DETERMINANT / MEMBRANE BINDING / CALCIUM BINDING | ||||||
Function / homology | ![]() phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / : / toxin activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Briggs, D.C. / Basak, A.K. | ||||||
![]() | ![]() Title: Clostridium Absonum Alpha-Toxin: New Insights Into Clostridial Phospholipase C Substrate Binding and Specificity Authors: Clark, G. / Briggs, D.C. / Karasawa, T. / Wang, X. / Cole, A. / Maegawa, T. / Jayasekera, P. / Naylor, C. / Miller, J. / Moss, D. / Nakamura, S. / Basak, A.K. / Titball, R. #1: ![]() Title: Structure of the Key Toxin in Gas Gangrene Authors: Naylor, C.E. / Eaton, J.T. / Howells, A. / Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | 249 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 484.4 KB | Display | |
Data in XML | ![]() | 54.4 KB | Display | |
Data in CIF | ![]() | 74.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ca1S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 42753.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 100MM NA-CITRATE 5.6, 30% PEG 4000,200MM AMMONIUM ACETATE, pH 5.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.784 Å / Num. obs: 53292 / % possible obs: 96.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2 / % possible all: 90 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 56134 / Num. measured all: 623268 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CA1 WITH LOOPS OMITTED Resolution: 2.5→29.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.818 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.786 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES/ATOMS WERE OMITTED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.75 Å
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Refine LS restraints |
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