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Yorodumi- PDB-1pzj: Cholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pzj | ||||||
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Title | Cholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5 | ||||||
Components | Cholera Toxin B Subunit | ||||||
Keywords | TOXIN / PENTAMER / MONOVALENT / INHIBITOR / CHOLERA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 | 1pzj.cif.gz | 247.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzj.ent.gz | 199.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pzj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1pzj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1pzj_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 1pzj_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzj ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzj | HTTPS FTP |
-Related structure data
Related structure data | 1pziC 1pzkC 3chbS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11623.267 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CAA41591 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q57193 #2: Chemical | #3: Chemical | #4: 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: 1.81 Å3/Da / Density % sol: 31.7 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 42% PEG 350, 50 mM NaCl, 100 mM Tris-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2002 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→99 Å / Num. all: 85036 / Num. obs: 85036 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.18 % / Biso Wilson estimate: 13.821 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.74 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 2.46 % / Mean I/σ(I) obs: 8.601 / Num. unique all: 8013 / Rsym value: 0.115 / % possible all: 93.2 |
Reflection | *PLUS Num. measured all: 274226 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 93.2 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 8.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CHB Resolution: 1.46→19.69 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.793 / SU ML: 0.032 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.059 / 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: 11.474 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→19.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.496 Å / Total num. of bins used: 20
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Refinement | *PLUS Rfactor Rfree: 0.159 / Rfactor Rwork: 0.115 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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