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- PDB-5g3l: ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g3l | |||||||||
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Title | ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMPLEXED WITH SIALYLATED SUGAR | |||||||||
![]() | (HEAT-LABILE ENTEROTOXIN IIB, B ...) x 2 | |||||||||
![]() | TOXIN / ENTEROTOXIN / ECOLI / B SUBUNIT / SIALIC ACID | |||||||||
Function / homology | ![]() perturbation of signal transduction in another organism / host cell membrane / toxin activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zalem, D. / Benktander, J. / Ribeiro, J.P. / Varrot, A. / Lebens, M. / Imberty, A. / Teneberg, S. | |||||||||
![]() | ![]() Title: Biochemical and Structural Characterization of the Novel Sialic Acid-Binding Site of Escherichia Coli Heat-Labile Enterotoxin Lt-Iib. Authors: Zalem, D. / Ribeiro, J.P. / Varrot, A. / Lebens, M. / Imberty, A. / Teneberg, S. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tiiS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-HEAT-LABILE ENTEROTOXIN IIB, B ... , 2 types, 5 molecules DEHFG
#1: Protein | Mass: 10794.190 Da / Num. of mol.: 3 / Fragment: RESIDUES 24-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 10778.190 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/SIA.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 2 types, 593 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | TERMINAL GLUTAMATE WAS CLEAVED IN SOME CHAINS. OXIDATION WAS OBSERVED IN METHIONINE69. THE ...TERMINAL GLUTAMATE WAS CLEAVED IN SOME CHAINS. OXIDATION WAS OBSERVED IN METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 20% PEG3350, 0.2M KCL, 0.1M NA2CO3, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→48.56 Å / Num. obs: 54271 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TII Resolution: 1.72→46.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.29 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 17.705 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→46.33 Å
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Refine LS restraints |
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