+Open data
-Basic information
Entry | Database: PDB / ID: 1ca1 | ||||||
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Title | ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS | ||||||
Components | ALPHA-TOXIN | ||||||
Keywords | HYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase C activity / phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / toxin activity / killing of cells of another organism / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR, MOLECULAR REPLACEMENT, CROSS-CRYSTAL AVERAGING / Resolution: 1.9 Å | ||||||
Authors | Naylor, C.E. / Basak, A.K. / Titball, R.W. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Alpha-Toxin from Two Different Strains (Nctc8237 and Cer89L43) of Clostridium Perfringens Authors: Basak, A.K. / Howells, A. / Eaton, J.T. / Moss, D.S. / Naylor, C.E. / Miller, J. / Titball, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ca1.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ca1.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ca1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ca1_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 1ca1_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 1ca1_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1ca1_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/1ca1 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/1ca1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42615.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: CER89L43 / Gene: CPA / Plasmid: PUC18 / Cellular location (production host): PERIPLASMIC / Gene (production host): CPA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P15310, UniProt: P0C216*PLUS, phospholipase C | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-CD / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % Description: EARLIER MODEL WILL BE DEPOSITED AFTER FULL REFINEMENT. SIR CARRIED OUT ON ALTERNATE CRYSTAL FORM WHICH WILL ALSO BE DEPOSITED IN NEAR FUTURE. | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL OR NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 30175 / % possible obs: 87.5 % / Observed criterion σ(I): -3 / Redundancy: 5.26 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.96 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.3 / % possible all: 73.8 |
Reflection | *PLUS % possible obs: 91 % / Num. measured all: 202958 |
-Processing
Software |
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Refinement | Method to determine structure: SIR, MOLECULAR REPLACEMENT, CROSS-CRYSTAL AVERAGING Starting model: INCOMPLETE EARLIER CHAIN TRACE OF ALTERNATE STRAIN Resolution: 1.9→25 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED B-F / Cross valid method: USED THROUGHOUT REFINEMENT
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Displacement parameters | Biso mean: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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