+Open data
-Basic information
Entry | Database: PDB / ID: 5x7y | ||||||
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Title | Crystal Structure of the Dog Lipocalin Allergen Can f 6 | ||||||
Components | Lipocalin-Can f 6 allergen | ||||||
Keywords | ALLERGEN / lipocalin allergen | ||||||
Function / homology | Function and homology information odorant binding / small molecule binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Yamamoto, K. / Otani, T. / Sugiura, K. / Nakatsuji, M. / Nishimura, S. / Inui, T. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Crystal structure of the dog allergen Can f 6 and structure-based implications of its cross-reactivity with the cat allergen Fel d 4. Authors: Yamamoto, K. / Ishibashi, O. / Sugiura, K. / Ubatani, M. / Sakaguchi, M. / Nakatsuji, M. / Shimamoto, S. / Noda, M. / Uchiyama, S. / Fukutomi, Y. / Nishimura, S. / Inui, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x7y.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x7y.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x7y ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x7y | HTTPS FTP |
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-Related structure data
Related structure data | 1gm6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 20361.941 Da / Num. of mol.: 4 / Fragment: UNP residues 16-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: lcn / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H2B3G5 #2: Chemical | ChemComp-PEG / #3: 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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.0 M ammonium dihydrogenphosphate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→96.6 Å / Num. obs: 32931 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.952 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.028 / Χ2: 2.538 / Net I/σ(I): 52.2 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 14.3 % / Num. unique obs: 1615 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GM6 Resolution: 2.35→96.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.367 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.26 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.849 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→96.6 Å
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Refine LS restraints |
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