+Open data
-Basic information
Entry | Database: PDB / ID: 5fds | |||||||||
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Title | Crystal structure of the monomeric allergen profilin (Hev b 8) | |||||||||
Components | Profilin-2 | |||||||||
Keywords | ALLERGEN / Actin Binding Protein / Allergy / Cross-reactivity / Hev b 8 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Hevea brasiliensis (rubber tree) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Mares-Mejia, I. / Rodriguez-Romero, A. | |||||||||
Funding support | Mexico, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural insights into the IgE mediated responses induced by the allergens Hev b 8 and Zea m 12 in their dimeric forms. Authors: Mares-Mejia, I. / Martinez-Caballero, S. / Garay-Canales, C. / Cano-Sanchez, P. / Torres-Larios, A. / Lara-Gonzalez, S. / Ortega, E. / Rodriguez-Romero, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fds.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fds.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fds ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fds | HTTPS FTP |
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-Related 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: 14162.038 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Clone RRIM600 / Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Tissue: Leaf / Gene: PRO2 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9STB6 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M TRIS-HCL, pH 9.0, 1.6 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5416 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5416 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.22 Å / Num. obs: 19125 / % possible obs: 98.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.7 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.12 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→33.22 Å
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Refine LS restraints |
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LS refinement shell |
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