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- PDB-1rcv: 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: 1rcv | ||||||
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Title | Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1 | ||||||
![]() | 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 | ![]() | 122.1 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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-BV1 / [ #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG 300, 50 mM NaCl, 100 mM Tris-HCl, and 2.3mM BV1, 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: May 16, 2003 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 66250 / Num. obs: 63041 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3 / Num. unique all: 4963 / % possible all: 76.3 |
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Processing
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Refinement | Resolution: 1.6→41.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.832 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: 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: 11.201 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→41.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.64 Å / Total num. of bins used: 20 /
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