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Yorodumi- PDB-1rf2: Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Gala... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rf2 | ||||||
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Title | Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4 | ||||||
Components | cholera toxin B protein (CTB) | ||||||
Keywords | TOXIN / Bivalent / Cholera / Pentamer / Complex | ||||||
Function / homology | Function and homology information host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pickens, J.C. / Mitchell, D.D. / Liu, J. / Tan, X. / Zhang, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E. | ||||||
Citation | Journal: Chem.Biol. / Year: 2004 Title: Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer. Authors: Pickens, J.C. / Mitchell, D.D. / Liu, J. / Tan, X. / Zhang, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rf2.cif.gz | 243.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rf2.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rf2 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rf2 | HTTPS FTP |
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-Related structure data
Related structure data | 1rcvC 1rd9C 1rdpC 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: ctxB / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P01556 #2: Chemical | ChemComp-BV4 / #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-PGE / | #5: 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: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9626 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2003 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9626 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 111363 / Num. obs: 104314 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7606 / % possible all: 69.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CHB Resolution: 1.35→49.39 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.934 / SU ML: 0.037 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Maximum Likelihood
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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: 10.455 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.347→1.382 Å / Total num. of bins used: 20
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