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Yorodumi- PDB-1lt6: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lt6 | ||||||
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Title | HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYLGALACTOSIDE | ||||||
Components | HEAT-LABILE ENTEROTOXIN | ||||||
Keywords | ENTEROTOXIN | ||||||
Function / homology | Function and homology information toxin activity / killing of cells of another organism / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Merritt, E.A. / Hol, W.G.J. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin. Authors: Merritt, E.A. / Sarfaty, S. / Feil, I.K. / Hol, W.G. #1: Journal: Mol.Microbiol. / Year: 1994 Title: Galactose-Binding Site in Escherichia Coli Heat-Labile Enterotoxin (Lt) and Cholera Toxin (Ct) Authors: Merritt, E.A. / Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Hol, W.G. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Refined Structure of Escherichia Coli Heat-Labile Enterotoxin, a Close Relative of Cholera Toxin Authors: Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lt6.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lt6.ent.gz | 177.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lt6_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 1lt6_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 1lt6_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 1lt6_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1lt6 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1lt6 | HTTPS FTP |
-Related structure data
Related structure data | 1lt5C 1ltaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11807.539 Da / Num. of mol.: 10 / Fragment: B-PENTAMER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890 #2: Sugar | ChemComp-GAA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: three-layered solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1996 / Details: DOUBLY-FOCUSED MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 51781 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 2.23 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.298 / % possible all: 71.8 |
Reflection shell | *PLUS % possible obs: 72 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LTA Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BABINET BULK SOLVENT MODEL
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Displacement parameters | Biso mean: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.23 Å / Total num. of bins used: 15 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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