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- PDB-1qnu: Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qnu | |||||||||
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Title | Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor | |||||||||
![]() | Shiga toxin 1 variant B subunit | |||||||||
![]() | TOXIN / SUBNANOMOLAR INHIBITOR / MULTIVALENT PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD | |||||||||
Function / homology | ![]() modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / : / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pannu, N.S. / Hayakawa, K. / Read, R.J. | |||||||||
![]() | ![]() Title: Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands. Authors: Kitov, P.I. / Sadowska, J.M. / Mulvey, G. / Armstrong, G.D. / Ling, H. / Pannu, N.S. / Read, R.J. / Bundle, D.R. #1: ![]() Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Bg3 Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / 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 | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bosS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | BIOLOGICAL_UNIT: PENTAMER |
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Components
#1: Protein | Mass: 7698.634 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH BRIDGE-STARFISH MOLECULE, A SUBNANOMOLAR TAILORED MULTIVALENT INHIBITOR Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EMB / #4: Chemical | ChemComp-MEC / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION ...Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (28% SA NH4SO4, 2% 2-METHYL-2,4-PENTANEDIOL, 0.1M NACL, 0.1 M HEPES, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 19159 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 2.23→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.291 / % possible all: 96.2 |
Reflection | *PLUS Rmerge(I) obs: 0.161 |
Reflection shell | *PLUS Lowest resolution: 2.34 Å / % possible obs: 94.9 % / Rmerge(I) obs: 0.339 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BOS Resolution: 2.23→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1625101.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.4401 Å2 / ksol: 0.411496 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.23→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 4.81 Å2 / Rms dev position: 0.25 Å / Weight Biso : 1 / Weight position: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.23→2.37 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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