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Yorodumi- PDB-1pzi: Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Gal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pzi | ||||||
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Title | Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Galactoside 2a | ||||||
Components | Heat-labile Enterotoxin B subunit | ||||||
Keywords | TOXIN INHIBITOR / PENTAMER / MONOVALENT / TOXIN / INHIBITOR | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Mitchell, D.D. / Pickens, J.C. / Korotkov, K. / Fan, E. / Hol, W.G.J. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2004 Title: 3,5-Substituted phenyl galactosides as leads in designing effective cholera toxin antagonists; synthesis and crystallographic studies Authors: Mitchell, D.D. / Pickens, J.C. / Korotkov, K. / Fan, E. / 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 | 1pzi.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzi.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzi ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzi | HTTPS FTP |
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-Related structure data
Related structure data | 1pzjC 1pzkC 1djrS C: citing same article (ref.) S: Starting model for refinement |
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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: 11807.539 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ELTB / Plasmid: LAMBDA-PR / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P32890 #2: Chemical | ChemComp-1DM / #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: 1.96 Å3/Da / Density % sol: 36.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 32% PEG 5000, 100 mM Tris-HCl pH 7.8, 50 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 23, 2002 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. all: 34499 / Num. obs: 34499 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 20.322 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.28 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 2.27 % / Mean I/σ(I) obs: 7.07 / Num. unique all: 3005 / Rsym value: 0.145 / % possible all: 84.1 |
Reflection | *PLUS Num. measured all: 124930 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 84.1 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DJR Resolution: 1.99→27.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.336 / SU ML: 0.121 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.192 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→27.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.041 Å / Total num. of bins used: 20
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Refinement | *PLUS Rfactor Rfree: 0.221 / Rfactor Rwork: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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