+Open data
-Basic information
Entry | Database: PDB / ID: 1olp | ||||||
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Title | Alpha Toxin from Clostridium Absonum | ||||||
Components | ALPHA-TOXIN | ||||||
Keywords | HYDROLASE / ZINC PHOSPHOLIPASE C / GAS GANGRENE DETERMINANT / MEMBRANE BINDING / CALCIUM BINDING | ||||||
Function / homology | Function and homology information phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / : / toxin activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM SARDINIENSE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Briggs, D.C. / Basak, A.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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: Journal: Nat.Struct.Biol. / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1olp.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1olp.ent.gz | 249 KB | Display | PDB format |
PDBx/mmJSON format | 1olp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/1olp ftp://data.pdbj.org/pub/pdb/validation_reports/ol/1olp | HTTPS FTP |
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-Related structure data
Related structure data | 1ca1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) CLOSTRIDIUM SARDINIENSE (bacteria) / Description: CLOSTRIDIUM ABSONUM / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8GCY3, phospholipase C #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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