+Open data
-Basic information
Entry | Database: PDB / ID: 8aeh | ||||||
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Title | X-ray structure of Canis familiaris Odorant Binding Protein 1 | ||||||
Components | Major allergen Can f 1 | ||||||
Keywords | TRANSPORT PROTEIN / Odorant binding protein | ||||||
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: 3 Å | ||||||
Authors | Schwartz, M. / Briand, L. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Structure of dog odorant binding protein Authors: Glaz, M. / Schwartz, M. / Briand, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aeh.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aeh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8aeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aeh_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 8aeh_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 8aeh_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 8aeh_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8aeh ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8aeh | HTTPS FTP |
-Related structure data
Related structure data | 8aeiC 8aejC 3eycS S: Starting model for refinement 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
#1: Protein | Mass: 18915.330 Da / Num. of mol.: 1 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: Chemical | ChemComp-CA / |
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: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 4000, 0.2 M CaCl2 in 0.1 M pH 8.5 Tris buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.11 Å / Num. obs: 3242 / % possible obs: 100 % / Redundancy: 25 % / Biso Wilson estimate: 69.57 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.014 / Rrim(I) all: 0.067 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 14.5 / Num. unique obs: 512 / CC1/2: 0.997 / Rpim(I) all: 0.038 / Rrim(I) all: 0.192 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EYC Resolution: 3→44.11 Å / SU ML: 0.3672 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 27.3134 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: 62.28 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.11 Å
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Refine LS restraints |
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LS refinement shell |
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