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Open data
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Basic information
Entry | Database: PDB / ID: 2bos | |||||||||
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Title | A MUTANT SHIGA-LIKE TOXIN IIE BOUND TO ITS RECEPTOR | |||||||||
![]() | PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT) | |||||||||
![]() | TOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / SPECIFICITY | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ling, H. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J. | |||||||||
![]() | ![]() Title: A mutant Shiga-like toxin IIe bound to its receptor Gb(3): structure of a group II Shiga-like toxin with altered binding specificity. Authors: Ling, H. / Pannu, N.S. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J. #1: ![]() Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Gb3 Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J. #2: ![]() Title: Crystal Structure of the Cell-Binding B Oligomer of Verotoxin-1 from E. Coli Authors: Stein, P.E. / Boodhoo, A. / Tyrrell, G.J. / Brunton, J.L. / Read, R.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
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PDB format | ![]() | 67.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qohC ![]() 1bov S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
#1: Protein | Mass: 7590.411 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: Q65E, K67Q Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE) Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 51.23 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.4 Details: PROTEIN WAS CRYSTALLIZED FROM 1 M NACL,10 MM TRIS-HCL BUFFE, pH 8.4 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1994 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→31 Å / Num. obs: 25704 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 1.66 / Rsym value: 0.216 / % possible all: 82.4 |
Reflection | *PLUS Num. measured all: 308496 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS Lowest resolution: 2.15 Å / % possible obs: 87.2 % / Rmerge(I) obs: 0.222 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BOV ![]() 1bov Resolution: 2→31 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: CROSS-VALIDATION DATA ARE LIKELY TO BE SOMEWHAT OVER-FIT BECAUSE OF 5-FOLD NCS.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→31 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 3.5
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 2541 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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