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Yorodumi- PDB-1eei: CHOLERA TOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL-ALPHA-D-G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eei | ||||||
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Title | CHOLERA TOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL-ALPHA-D-GALACTOSE | ||||||
Components | PROTEIN (CHOLERA TOXIN B) | ||||||
Keywords | TOXIN / ENTEROTOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 2 Å | ||||||
Authors | Merritt, E.A. / Hol, W.G.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Exploration of the GM1 receptor-binding site of heat-labile enterotoxin and cholera toxin by phenyl-ring-containing galactose derivatives. Authors: Fan, E. / Merritt, E.A. / Zhang, Z. / Pickens, J.C. / Roach, C. / Ahn, M. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 1998 Title: The 1.25 A Resolution Refinement of the Cholera Toxin B-Pentamer: Evidence of Peptide Backbone Strain at the Receptor-binding Site. Authors: Merritt, E.A. / Kuhn, P. / Sarfaty, S. / Erbe, J.L. / Holmes, R.K. / Hol, W.G. #2: Journal: Structure / Year: 1997 Title: Structural Foundation for the Design of Receptor Antagonists Targeting Escherichia Heat-Labile Enterotoxin Authors: Merritt, E.A. / Sarfaty, S. / Feil, I.K. / Hol, W.G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eei.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eei.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eei_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 1eei_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 1eei_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1eei_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eei ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eei | HTTPS FTP |
-Related structure data
Related structure data | 1eefC 1efiC 1fd7C 3chbS 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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Unit cell |
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-Components
#1: Protein | Mass: 11623.267 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: RECEPTOR BINDING SITE ON EACH MONOMER OCCUPIED BY METANITROPHENYL-ALPHA-D-GALACTOSIDE Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OGAWA 41 (CLASSICAL BIOTYPE) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57193 #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: 2.56 Å3/Da / Density % sol: 54.32 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: SITTING DROP, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 10, 1998 / Details: DOUBLE-FOCUS MIRRORS MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 40887 / Num. obs: 40887 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3785 / % possible all: 88 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 88 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: PDB ENTRY 3CHB Resolution: 2→20 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 1 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |