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Yorodumi- PDB-8aei: X-ray structure of Canis familiaris Odorant Binding Protein 2 bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aei | ||||||
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Title | X-ray structure of Canis familiaris Odorant Binding Protein 2 bound to citronellal | ||||||
Components | Minor allergen Can f 2 | ||||||
Keywords | TRANSPORT PROTEIN / Odorant binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 | 8aei.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aei.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 8aei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aei_validation.pdf.gz | 823.2 KB | Display | wwPDB validaton report |
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Full document | 8aei_full_validation.pdf.gz | 824.5 KB | Display | |
Data in XML | 8aei_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 8aei_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8aei ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8aei | HTTPS FTP |
-Related structure data
Related structure data | 8aehC 8aejC 3l4rS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19974.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18874 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.03 Å3/Da / Density % sol: 39.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 35% PEG 4000, 0.2 M MgCl2 in 0.1 M pH 8.0 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: 0.978566 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978566 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→48.69 Å / Num. obs: 32275 / % possible obs: 97 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.376 / Num. unique obs: 1535 / CC1/2: 0.949 / Rpim(I) all: 0.153 / Rrim(I) all: 0.407 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L4R Resolution: 1.74→38.91 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5942 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: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→38.91 Å
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Refine LS restraints |
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LS refinement shell |
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