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- PDB-7prp: Crystal Structure of the B subunit of heat labile enterotoxin LT-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7prp | ||||||
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Title | Crystal Structure of the B subunit of heat labile enterotoxin LT-IIc from Escherichia coli in apo form | ||||||
![]() | Heat-labile enterotoxin IIA, B chain | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / ganglioside / heat labile enterotoxin | ||||||
Function / homology | Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / extracellular region / FORMIC ACID / Heat-labile enterotoxin IIA, B chain![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Varrot, A. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Characterization of the ganglioside recognition profile of Escherichia coli heat-labile enterotoxin LT-IIc. Authors: Zalem, D. / Juhas, M. / Terrinoni, M. / King-Lyons, N. / Lebens, M. / Varrot, A. / Connell, T.D. / Teneberg, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7prsC ![]() 5g3lS 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 domain segments: Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 104 / Label seq-ID: 1 - 104
NCS ensembles :
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Components
#1: Protein | Mass: 11499.999 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Mature protein. numbering does not include peptide signal Source: (gene. exp.) ![]() ![]() Gene: LT-IIc1 B, GQM13_12885, HVV37_03950, HVV78_10285, HVW37_13205 Plasmid: pBC1 / Production host: ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.1 % / Description: needle |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.4 sodium formation and 100 mM citric acid pH 4.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42 Å / Num. obs: 24817 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.079 / Rrim(I) all: 0.125 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9279 / CC1/2: 0.806 / Rpim(I) all: 0.382 / Rrim(I) all: 0.597 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G3L Resolution: 2.3→41.981 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.87 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.246 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→41.981 Å
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Refine LS restraints |
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