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Yorodumi- PDB-8epu: 1.6 A crystal structure of the lipocalin dog allergen Can f 1 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8epu | ||||||
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Title | 1.6 A crystal structure of the lipocalin dog allergen Can f 1 with the C118S mutation | ||||||
Components | Major allergen Can f 1 | ||||||
Keywords | ALLERGEN / Lipocalin / Fatty acid binding protein / Calyx | ||||||
Function / homology | von Ebner's gland protein/ Bos/Can allergen / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / Major allergen Can f 1 Function and homology information | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Min, J. / Pedersen, L.C. / Geoffrey, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Allergy / Year: 2023 Title: Structural and ligand binding analysis of the pet allergens Can f 1 and Fel d 7. Authors: Min, J. / Foo, A.C.Y. / Gabel, S.A. / Perera, L. / DeRose, E.F. / Pomes, A. / Pedersen, L.C. / Mueller, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8epu.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8epu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8epu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8epu_validation.pdf.gz | 405.4 KB | Display | wwPDB validaton report |
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Full document | 8epu_full_validation.pdf.gz | 405.3 KB | Display | |
Data in XML | 8epu_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 8epu_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8epu ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8epu | HTTPS FTP |
-Related structure data
Related structure data | 8epvC 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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Details | The oligomeric state is unknown. Lipocalin proteins are often in a transient monomer to oligomer state. |
-Components
#1: Protein | Mass: 16569.699 Da / Num. of mol.: 1 / Mutation: C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18873 |
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#2: 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: 1.95 Å3/Da / Density % sol: 37.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35 % PEG 4000 |
-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: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 16064 / % possible obs: 94 % / Redundancy: 3.1 % / Biso Wilson estimate: 24.85 Å2 / CC1/2: 0.986 / Net I/σ(I): 25.98 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 684 / CC1/2: 0.975 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold Resolution: 1.6→31.34 Å / SU ML: 0.1854 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.3045 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 36.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→31.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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