+Open data
-Basic information
Entry | Database: PDB / ID: 8ti5 | ||||||
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Title | Crystal structure of Tyr p 36.0101 | ||||||
Components | Profilin | ||||||
Keywords | ALLERGEN / mite profilin / storage mite / allergy | ||||||
Function / homology | Function and homology information sequestering of actin monomers / actin monomer binding / cell cortex / cytoskeleton Similarity search - Function | ||||||
Biological species | Tyrophagus putrescentiae (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | O'Malley, A. / Sankaran, S. / Chruszcz, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biol.Chem. / Year: 2024 Title: Structural homology of mite profilins to plant profilins is not indicative of allergic cross-reactivity. Authors: O'Malley, A. / Sankaran, S. / Carriuolo, A. / Khatri, K. / Kowal, K. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ti5.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ti5.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 8ti5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/8ti5 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/8ti5 | HTTPS FTP |
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-Related structure data
Related structure data | 8ti6C 8ti7C 8v5yC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14410.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tyrophagus putrescentiae (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2YLJ4 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid pH 3.5, 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→40 Å / Num. obs: 47953 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Rsym value: 0.06 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 1.15→1.17 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1441 / CC1/2: 0.919 / CC star: 0.979 / Rpim(I) all: 0.164 / Rrim(I) all: 0.349 / Rsym value: 0.304 / % possible all: 57.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→30.462 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.107 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.037 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.857 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→30.462 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: 20
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