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- 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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![]() | 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![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 877.9 KB | Display | ![]() |
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PDB format | ![]() | 736.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.3 KB | Display | ![]() |
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Full document | ![]() | 509.9 KB | Display | |
Data in XML | ![]() | 85.6 KB | Display | |
Data in CIF | ![]() | 112.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9nphC ![]() 9npiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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.) ![]() ![]() ![]() #2: Antibody | Mass: 23392.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]()
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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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