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Yorodumi- PDB-4o4x: Crystal structure of the vaccine antigen Transferrin Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o4x | ||||||
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Title | Crystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) double mutant Tyr-167-Ala and Trp-176-Ala from Haemophilus parasuis Hp5 | ||||||
Components | TbpB | ||||||
Keywords | METAL TRANSPORT / Structure-based vaccine design / transferrin receptor / iron acquisition / host pathogen interaction / surface lipoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus parasuis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 4o4x.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o4x.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o4x ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o4x | HTTPS FTP |
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-Related structure data
Related structure data | 4o3wC 4o3xC 4o3yC 4o3zC 4o49C 4o4uC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58295.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus parasuis (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UKY6*PLUS #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / | #5: 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: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.08 M potassium phosphate monobasic, 18% PEG 8000, 20% 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: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→42.182 Å / Num. obs: 26504 / Biso Wilson estimate: 57.75 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→42.182 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.41 / σ(F): 1.35 / Phase error: 24.09 / 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 mean: 55.5643 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→42.182 Å
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Refine LS restraints |
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LS refinement shell |
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