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Yorodumi- PDB-4o3y: Crystal structure of the vaccine antigen Transferrin Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o3y | ||||||
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Title | Crystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Arg-179-Glu from Actinobacillus pleuropneumoniae H87 | ||||||
Components | Outer membrane protein; transferrin-binding protein | ||||||
Keywords | METAL TRANSPORT / Structure-based vaccine design / transferrin receptor / iron acquisition / host pathogen interaction / surface lipoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Actinobacillus pleuropneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Calmettes, C. / Yu, R.H. / Schryvers, A.B. / Moraes, T.F. | ||||||
Citation | Journal: Infect.Immun. / Year: 2015 Title: Nonbinding site-directed mutants of transferrin binding protein B exhibit enhanced immunogenicity and protective capabilities. Authors: Frandoloso, R. / Martinez-Martinez, S. / Calmettes, C. / Fegan, J. / Costa, E. / Curran, D. / Yu, R.H. / Gutierrez-Martin, C.B. / Rodriguez-Ferri, E.F. / Moraes, T.F. / Schryvers, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o3y.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o3y.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o3y ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o3y | HTTPS FTP |
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-Related structure data
Related structure data | 4o3wC 4o3xC 4o3zC 4o49C 4o4uC 4o4xC 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
#1: Protein | Mass: 57468.684 Da / Num. of mol.: 1 / Fragment: UNP residues 25-547 / Mutation: R179E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria) Gene: tfbA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44167 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 3.98 Å3/Da / Density % sol: 69.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.16 M sodium acetate, 0.08 M calcium cacodylate, 23% PEG 3350, 15% glycerol, pH 6.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Detector: CCD / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.655 Å / Num. obs: 30052 / Biso Wilson estimate: 47.81 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.655 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.39 / σ(F): 2.01 / Phase error: 25.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.58 Å2 / Biso mean: 56.3817 Å2 / Biso min: 15.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.655 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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