+Open data
-Basic information
Entry | Database: PDB / ID: 1jr0 | ||||||
---|---|---|---|---|---|---|---|
Title | CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011 | ||||||
Components | cholera toxin B subunit | ||||||
Keywords | TOXIN / ENTEROTOXIN / RECEPTOR / B-PENTAMER | ||||||
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 / Resolution: 1.3 Å | ||||||
Authors | Merritt, E.A. / Hol, W.G.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2002 Title: Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes. Authors: Pickens, J.C. / Merritt, E.A. / Ahn, M. / Verlinde, C.L. / Hol, W.G. / Fan, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jr0.cif.gz | 247.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jr0.ent.gz | 201.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jr0 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jr0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1jqyC 3chbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P01556 #2: Chemical | ChemComp-A24 / ( #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 43.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3000, NaCl, MgCl2, Tris HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→22 Å / Num. obs: 110275 / % possible obs: 89 % / Redundancy: 4 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.3→1.34 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4097 / % possible all: 40 |
Reflection | *PLUS Highest resolution: 1.3 Å |
Reflection shell | *PLUS % possible obs: 40 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 3CHB Resolution: 1.3→22 Å / Num. parameters: 44038 / Num. restraintsaints: 52704 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 4085 / Occupancy sum non hydrogen: 4925 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→22 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 104753 / Rfactor Rwork: 0.1307 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |