+Open data
-Basic information
Entry | Database: PDB / ID: 1r4q | ||||||
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Title | Shiga toxin | ||||||
Components |
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Keywords | TOXIN / AB5 toxin | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / metabolic process / 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 / Molecular replacement, SIR, averaging / Resolution: 2.5 Å | ||||||
Authors | Fraser, M.E. / Fujinaga, M. / Cherney, M.M. / Melton-Celsa, A.R. / Twiddy, E.M. / O'Brien, A.D. / James, M.N.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure of Shiga Toxin Type 2 (Stx2) from Escherichia coli O157:H7. Authors: Fraser, M.E. / Fujinaga, M. / Cherney, M.M. / Melton-Celsa, A.R. / Twiddy, E.M. / O'Brien, A.D. / James, M.N.G. | ||||||
History |
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Remark 999 | sequence the authors maintain that the sequence database reference is incorrect at this position |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4q.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4q.ent.gz | 200.7 KB | Display | PDB format |
PDBx/mmJSON format | 1r4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r4q_validation.pdf.gz | 502.2 KB | Display | wwPDB validaton report |
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Full document | 1r4q_full_validation.pdf.gz | 534.3 KB | Display | |
Data in XML | 1r4q_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 1r4q_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4q ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32264.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Plasmid: PSHT23 / 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) / Plasmid: PSHT23 / 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: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM CITRATE, ETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
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→98.6 Å / Num. all: 56837 / Num. obs: 53525 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.66 Å / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular replacement, SIR, averaging Resolution: 2.5→98.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→98.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02
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