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Open data
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Basic information
Entry | Database: PDB / ID: 5lzg | ||||||
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Title | Cholera toxin El Tor B-pentamer in complex with inhibitor PC262 | ||||||
![]() | Cholera enterotoxin subunit B | ||||||
![]() | TOXIN / cholera toxin B-pentamer / inhibitor | ||||||
Function / homology | ![]() host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heggelund, J.E. / Martinsen, T. / Krengel, U. | ||||||
![]() | ![]() Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.6 KB | Display | ![]() |
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PDB format | ![]() | 190.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lzhC ![]() 5lziC ![]() 5lzjC ![]() 3chbS 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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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 11660.348 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ctxB, toxB, VC_1456 / Production host: ![]() |
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-Non-polymers , 6 types, 585 molecules ![](data/chem/img/7BN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-7BN / ( #3: Chemical | ChemComp-TRS / | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-MRD / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES/Imidazole buffer, pH 6.5, 10% PEG 1000, 10 % PEG 3350, 10 % MPD, 0.03 M divalent cations |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991872 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→47.8 Å / Num. obs: 139423 / % possible obs: 74.3 % / Redundancy: 2.7 % / CC1/2: 0.999 / Net I/σ(I): 8.94 |
Reflection shell | Resolution: 1.12→1.19 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.359 / % possible all: 13.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CHB Resolution: 1.13→47.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.431 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.565 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→47.8 Å
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Refine LS restraints |
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