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Yorodumi- PDB-2j42: low quality crystal structure of the transport component C2-II of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j42 | ||||||
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Title | low quality crystal structure of the transport component C2-II of the C2-toxin from Clostridium botulinum | ||||||
Components | C2 TOXIN COMPONENT-II | ||||||
Keywords | TOXIN / CLOSTRIDIUM BOTULINUM / C2-II | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CLOSTRIDIUM BOTULINUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure and Action of the Binary C2 Toxin from Clostridium Botulinum. Authors: Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j42.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j42.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 2j42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j42_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 2j42_full_validation.pdf.gz | 502.6 KB | Display | |
Data in XML | 2j42_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 2j42_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j42 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j42 | HTTPS FTP |
-Related structure data
Related structure data | 2j3vC 2j3xC 2j3zC 1accS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 80766.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O86171 |
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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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 4.6 Details: PROTEIN: 3 MG/ML IN H2O RESERVOIR: 0.1 M SODIUM ACETATE PH 4.6, 1.5 M (NH4)2SO4, 5 % ISOPROPANOL, 3 % ETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. obs: 15486 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 3.13→3.22 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ACC Resolution: 3.13→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: INCOMPLETE MODEL, MISSING ATOM STRUCTURE WAS USED. MODEL IS OF LOW QUALITY DUE TO THE LOW RESOLUTION, NO FURTHER REFINEMENT WAS POSSIBLE.
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Refinement step | Cycle: LAST / Resolution: 3.13→30 Å
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