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Open data
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Basic information
Entry | Database: PDB / ID: 1bos | |||||||||
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Title | SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR | |||||||||
![]() | SHIGA-LIKE TOXIN I B SUBUNIT | |||||||||
![]() | TOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD | |||||||||
Function / homology | ![]() modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J. | |||||||||
![]() | ![]() 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. #1: ![]() 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 | ![]() | 317 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13.9 MB | Display | ![]() |
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Full document | ![]() | 13.9 MB | Display | |
Data in XML | ![]() | 52.3 KB | Display | |
Data in CIF | ![]() | 77 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bov S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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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: 7698.634 Da / Num. of mol.: 20 / Fragment: RECEPTOR-BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE) Source: (gene. exp.) Phage h30, Enterobacteria phage H-19B / Genus: , Lambda-like viruses / Species: , / Strain: , / Production host: ![]() ![]() #2: Polysaccharide | alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-GAL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 60 % Description: ALTHOUGH THE HIGH RESOLUTION DATA HAVE VERY POOR STATISTICS, A STATISTICAL ANALYSIS PRESENTED IN THE STRUCTURE REPORT INDICATED USEFUL INFORMATION TO 2.8 ANGSTROMS RESOLUTION |
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Crystal grow | pH: 6 / Details: pH 6.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→21 Å / Num. obs: 41759 / % possible obs: 81.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.176 / Rsym value: 0.176 / Net I/σ(I): 3.37 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 0.581 / Rsym value: 0.476 / % possible all: 57.3 |
Reflection | *PLUS Num. measured all: 113473 |
Reflection shell | *PLUS % possible obs: 57.3 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1BOV ![]() 1bov Resolution: 2.8→21 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 THE HIGH DEGREE OF NCS. CARBOHYDRATE PARAMETER AND TOPOLOGY FILES PARAM3.CHO AND TOPH3_MOD.CHO WERE OBTAINED FROM BILL WEIS.
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Refinement step | Cycle: LAST / Resolution: 2.8→21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1
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LS refinement shell | Resolution: 2.8→2.9 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.288 |