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- PDB-5lzh: Cholera toxin classical B-pentamer in complex with inhibitor PC262 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lzh | |||||||||
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Title | Cholera toxin classical B-pentamer in complex with inhibitor PC262 | |||||||||
![]() | (Cholera enterotoxin B ...) x 2 | |||||||||
![]() | TOXIN / cholera toxin B-pentamer / inhibitor | |||||||||
Function / homology | ![]() | |||||||||
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 | ![]() | 238.6 KB | Display | ![]() |
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PDB format | ![]() | 192.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lzgC ![]() 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
-Cholera enterotoxin B ... , 2 types, 5 molecules ABDCE
#1: Protein | Mass: 11655.267 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244 Production host: ![]() ![]() #2: Protein | Mass: 11623.267 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ctxB, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244 Production host: ![]() ![]() |
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-Non-polymers , 6 types, 619 molecules ![](data/chem/img/7BN.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-7BN / ( #4: Chemical | ChemComp-MRD / ( | #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES/Imidazole pH 6.5, 8% PEG1000, 8% PEG 3350, 8% 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: 1.13→49 Å / Num. obs: 135800 / % possible obs: 73.7 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.87 |
Reflection shell | Resolution: 1.13→1.19 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.73 / CC1/2: 0.504 / % possible all: 13.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CHB Resolution: 1.13→73.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.685 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.606 Å2
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Refinement step | Cycle: 1 / Resolution: 1.13→73.55 Å
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Refine LS restraints |
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