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Open data
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Basic information
Entry | Database: PDB / ID: 1lti | |||||||||
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Title | HEAT-LABILE ENTEROTOXIN (LT-I) COMPLEX WITH T-ANTIGEN | |||||||||
![]() | (HEAT LABILE ENTEROTOXIN TYPE ...) x 3 | |||||||||
![]() | ENTEROTOXIN / ADP-RIBOSYL TRANSFERASE | |||||||||
Function / homology | ![]() toxin activity / killing of cells of another organism / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Van Den Akker, F. / Hol, W.G.J. | |||||||||
![]() | ![]() Title: Tumor marker disaccharide D-Gal-beta 1, 3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli. Authors: van den Akker, F. / Steensma, E. / Hol, W.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.4 KB | Display | ![]() |
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PDB format | ![]() | 129.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793.6 KB | Display | ![]() |
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Full document | ![]() | 811 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | THE ASYMMETRIC UNIT CONTAINS ONE AB5 TOXIN HEXAMER. THE A SUBUNIT CONTAINS TWO FRAGMENTS LINKED BY A DISORDERED LOOP. THESE 2 FRAGMENTS ARE CONVENTIONALLY REFERRED TO AS A1 AND A2, WHICH ARE LABELED AS CHAINS A AND C IN THIS COORDINATE SET. FRAGMENT A1 AND A2 ARE COVALENTLY LINKED IN THE LATENT TOXIN AND ARE PROTEOLYTICALLY CLEAVED UPON ACTIVATION. |
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Components
-HEAT LABILE ENTEROTOXIN TYPE ... , 3 types, 7 molecules DEFGHAC
#1: Protein | Mass: 11807.539 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: LATENT/INACTIVE FORM / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 22086.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LATENT/INACTIVE FORM / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | | Mass: 5783.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LATENT/INACTIVE FORM / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/GAL.gif)
#4: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen |
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#5: Sugar |
-Non-polymers , 1 types, 183 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Details
Nonpolymer details | D-GALACTOSE-BETA1,3-N-ACETYL-GALACTOSAMINE (GAL-BETA1, 3GALNAC) IS THE DISACCHARIDE PART OF THE ...D-GALACTOSE-BETA1,3-N-ACETYL-GALACTOSAM |
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Sequence details | SUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE A1 A 4 - 188 A2 C 196 - 236 B#1 D 1 - 103 ...SUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE A1 A 4 - 188 A2 C 196 - 236 B#1 D 1 - 103 B#2 E 1 - 103 B#3 F 1 - 103 B#4 G 1 - 103 B#5 H 1 - 103 WATER W 1 - 183 GALACTOSE D 104 GALACTOSE E 104 GALACTOSE G 104 N-ACETYL GALACTOSAM |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: liquid - liquid diffusion / pH: 7.5 Details: LIQUID-LIQUID DIFFUSION CAPILLARY CONTAINS: 0.1M TRIS PH 7.5, 0.1M NACL, 0.001M EDTA, 0.02% SODIUM AZIDE, 4.5 MG/ML LT-I, 0.025M LACTOSE AND 5% PEG 6000. CRYSTAL WAS SOAKED FOR 1 DAY IN ...Details: LIQUID-LIQUID DIFFUSION CAPILLARY CONTAINS: 0.1M TRIS PH 7.5, 0.1M NACL, 0.001M EDTA, 0.02% SODIUM AZIDE, 4.5 MG/ML LT-I, 0.025M LACTOSE AND 5% PEG 6000. CRYSTAL WAS SOAKED FOR 1 DAY IN LACTOSE FREE MOTHER LIQUOR CONTAINING 0.1M D-GAL-BETA1,3GALNAC BEFORE DATA COLLECTION., liquid - liquid diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: three-layer capillary | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→77 Å / Num. obs: 38264 / % possible obs: 86.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.13→2.25 Å / Rmerge(I) obs: 0.16 / % possible all: 73.5 |
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Processing
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Refinement | Resolution: 2.13→8 Å / Cross valid method: FREE-R / σ(F): 2
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Displacement parameters | Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 36311 / Num. reflection Rfree: 1932 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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