+Open data
-Basic information
Entry | Database: PDB / ID: 1dm0 | ||||||
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Title | SHIGA TOXIN | ||||||
Components |
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Keywords | TOXIN / AB5 STRUCTURE / POLYPEPTIDE A / BLOCKING / ACTIVE SITE | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region Similarity search - Function | ||||||
Biological species | Shigella dysenteriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: Crystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution. Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N. #1: Journal: Protein Toxin Structure, Parker, M.W., Ed. / Year: 1996 Title: X-ray Crystal Structure of the Shiga Toxin Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Purification and Crystallization of Shiga Toxin from Shigella dysenteriae Authors: Kozlov, Y.V. / Chernaia, M.M. / Fraser, M.E. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm0.cif.gz | 234.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm0.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dm0_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 1dm0_full_validation.pdf.gz | 508.5 KB | Display | |
Data in XML | 1dm0_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 1dm0_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm0 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm0 | 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
#1: Protein | Mass: 31561.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: Q7BQ99, UniProt: Q9FBI2*PLUS, rRNA N-glycosylase #2: Protein | Mass: 7698.634 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7BQ98 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal grow | *PLUS Details: Kozlov, Y.Z., (1993) J. Mol. Biol., 232, 704. |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 23, 1992 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. all: 47612 / Num. obs: 47612 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.67 Å / Num. unique all: 5446 / % possible all: 53.1 |
Reflection shell | *PLUS % possible obs: 53.1 % |
-Processing
Software |
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Refinement | Resolution: 2.5→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT dictionary / Details: Refinement with X-PLOR and TNT
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: 'X-PLOR, TNT' / Classification: refinement | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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