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Yorodumi- PDB-9npg: X-ray crystal structure of recombinant Can f 1-C100S in complex w... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9npg | ||||||
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| Title | X-ray crystal structure of recombinant Can f 1-C100S in complex with human IgE mAb 12F3 Fab | ||||||
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Keywords | ALLERGEN/IMMUNE SYSTEM / Can f 1-IgE / dog allergen / allergen-antibody complex / human antibody / IgE-Can f 1 complex / allergen-antibody interaction / ALLERGEN / ALLERGEN-IMMUNE SYSTEM complex | ||||||
| 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 | Homo sapiens (human)![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||
Authors | Khatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2025Title: Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations. Authors: Khatri, K. / Ball, A. / Glesner, J. / Linn, C. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Zhang, J. / Peebles Jr., R.S. / Borowski, T. / Mueller, G.A. / Chapman, M.D. / Smith, S.A. / ...Authors: Khatri, K. / Ball, A. / Glesner, J. / Linn, C. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Zhang, J. / Peebles Jr., R.S. / Borowski, T. / Mueller, G.A. / Chapman, M.D. / Smith, S.A. / Pomes, A. / Chruszcz, M. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9npg.cif.gz | 877.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9npg.ent.gz | 736.7 KB | Display | PDB format |
| PDBx/mmJSON format | 9npg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9npg_validation.pdf.gz | 499.3 KB | Display | wwPDB validaton report |
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| Full document | 9npg_full_validation.pdf.gz | 509.9 KB | Display | |
| Data in XML | 9npg_validation.xml.gz | 85.6 KB | Display | |
| Data in CIF | 9npg_validation.cif.gz | 112.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/9npg ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npg | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8vqfC ![]() 8vqgC ![]() 9nphC ![]() 9npiC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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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: Antibody | Mass: 24638.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: ![]() #2: Antibody | Mass: 23392.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: ![]() #3: Protein | Mass: 16512.646 Da / Num. of mol.: 4 / Mutation: C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.63 Å3/Da / Density % sol: 53 % |
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| Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2 M NaCl, 0.1 M sodium citrate tribasic dihydrate pH 4.2, 20% w/v PEG 8,000 conditions |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å |
| Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 29, 2023 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
| Reflection | Resolution: 3.12→40 Å / Num. obs: 46837 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.104 / Rrim(I) all: 0.278 / Net I/σ(I): 7.47 |
| Reflection shell | Resolution: 3.12→3.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2313 / CC1/2: 0.598 / CC star: 0.865 / Rpim(I) all: 0.314 / Rrim(I) all: 0.813 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→39.67 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.877 / SU B: 53.438 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / 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: 83.621 Å2
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| Refinement step | Cycle: 1 / Resolution: 3.12→39.67 Å
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| Refine LS restraints |
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United States, 1items
Citation



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