+Open data
-Basic information
Entry | Database: PDB / ID: 4fo2 | ||||||
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Title | Heat-labile enterotoxin LT-IIb-B5(T13I) mutant | ||||||
Components | Heat-labile enterotoxin IIB, B chain | ||||||
Keywords | TOXIN / B pentamer of LT-IIb T13I mutant | ||||||
Function / homology | Function and homology information perturbation of signal transduction in another organism / host cell membrane / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Cody, V. / Pace, J. / Nawar, H. / Liang, S. / Connell, T. / Hajishengallis, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding. Authors: Cody, V. / Pace, J. / Nawar, H.F. / King-Lyons, N. / Liang, S. / Connell, T.D. / Hajishengallis, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fo2.cif.gz | 376.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fo2.ent.gz | 311.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fo2_validation.pdf.gz | 579.6 KB | Display | wwPDB validaton report |
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Full document | 4fo2_full_validation.pdf.gz | 627.9 KB | Display | |
Data in XML | 4fo2_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 4fo2_validation.cif.gz | 103.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/4fo2 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4fo2 | HTTPS FTP |
-Related structure data
Related structure data | 4fnfC 4fp5C 1qb5S 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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Unit cell |
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-Components
#1: Protein | Mass: 10661.130 Da / Num. of mol.: 20 / Fragment: LT-IIb-B5 / Mutation: T13I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: DH5aF'Kan / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P43529 #2: Chemical | ChemComp-NA / #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 7.5 Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 60% tacsimate, microbatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.975 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 7, 2010 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.8 Å / Num. obs: 313200 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.035 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 0.9 / Num. unique all: 40708 / Rsym value: 0.79 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QB5 Resolution: 1.5→45.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.872 / SU ML: 0.069 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.088 / ESU R Free: 0.091 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.778 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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