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Yorodumi- PDB-5lzi: Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lzi | ||||||
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Title | Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146 | ||||||
Components | Heat-labile enterotoxin B chain | ||||||
Keywords | TOXIN / heat-labile enterotoxin / inhibitor / cholera | ||||||
Function / homology | Function and homology information toxin activity / killing of cells of another organism / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Heggelund, J.E. / Mackenzie, A. / 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 | 5lzi.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lzi.ent.gz | 202.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/5lzi ftp://data.pdbj.org/pub/pdb/validation_reports/lz/5lzi | HTTPS FTP |
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-Related structure data
Related structure data | 5lzgC 5lzhC 5lzjC 1efiS 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: 11788.492 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eltB, ltpB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32890 |
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-Non-polymers , 6 types, 822 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-7BQ / ( | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-7DB / ( #6: Chemical | ChemComp-PO4 / | #7: 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: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium cacodylate, PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.2 Å / Num. obs: 74271 / % possible obs: 92.9 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.902 / % possible all: 61.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFI Resolution: 1.6→29.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 67.76 Å2 / Biso mean: 17.9038 Å2 / Biso min: 5.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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