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Yorodumi- PDB-1kho: Crystal Structure Analysis of Clostridium perfringens alpha-Toxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kho | ||||||
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Title | Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP | ||||||
Components | alpha-toxin | ||||||
Keywords | TOXIN / N-terminal alpha-helix / C-terminal beta-sheet | ||||||
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 perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties. Authors: Justin, N. / Walker, N. / Bullifent, H.L. / Songer, G. / Bueschel, D.M. / Jost, H. / Naylor, C. / Miller, J. / 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 | 1kho.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kho.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1kho ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1kho | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 42421.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9RF12 #2: Chemical | ChemComp-ZN / #3: 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: 4.47 Å3/Da / Density % sol: 72.46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Na acetate, acetone, Na cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 60799 / Num. obs: 59406 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.4→2.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.8 / % possible all: 91.3 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 97.8 % / Num. measured all: 1381901 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Lowest resolution: 2.53 Å / % possible obs: 91.3 % / Rmerge(I) obs: 0.187 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a obs: 0.38 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 8 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.206 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.88 |