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- PDB-1rdp: Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Gala... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rdp | ||||||
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Title | Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3 | ||||||
![]() | cholera toxin B protein (CTB) | ||||||
![]() | TOXIN / Bivalent / Cholera / Pentamer / Complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pickens, J.C. / Mitchell, D.D. / Liu, J. / Tan, X. / Zhang, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.4 KB | Display | ![]() |
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PDB format | ![]() | 191.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rcvC ![]() 1rd9C ![]() 1rf2C ![]() 3chbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BV3 / #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2003 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 105335 / Num. obs: 100384 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6952 / % possible all: 63.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CHB Resolution: 1.35→48.22 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.942 / SU ML: 0.037 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.054 / 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: 10.928 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.351→1.386 Å / Total num. of bins used: 20
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