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Yorodumi- PDB-5lzj: Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lzj | ||||||
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Title | Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237 | ||||||
Components | Cholera enterotoxin subunit B | ||||||
Keywords | TOXIN / cholera toxin B-pentamer / inhibitor | ||||||
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 serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Heggelund, J.E. / Krengel, U. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lzj.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lzj.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/5lzj ftp://data.pdbj.org/pub/pdb/validation_reports/lz/5lzj | HTTPS FTP |
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-Related structure data
Related structure data | 5lzgC 5lzhC 5lziC 3chbS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 11660.348 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Gene: ctxB, toxB, VC_1456 / Production host: Vibrio sp. (bacteria) / References: UniProt: P01556 |
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-Non-polymers , 5 types, 556 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6, 30% PEG 400, 3% PGA-LM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→45.6 Å / Num. obs: 144269 / % possible obs: 93.8 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.55 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 2.3 % / CC1/2: 0.337 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CHB Resolution: 1.2→73.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.441 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.371 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→73.45 Å
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