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- PDB-8bxw: Crystal structure of Odorant Binding Protein 5 from Anopheles gam... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bxw | |||||||||
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Title | Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Carvacrol | |||||||||
![]() | Odorant binding protein | |||||||||
![]() | TRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction / Carvacrol | |||||||||
Function / homology | ![]() dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of AgamOBP5 in complex with the natural insect repellents Carvacrol and Thymol: Crystallographic, fluorescence and thermodynamic binding studies. Authors: Liggri, P.G.V. / Tsitsanou, K.E. / Stamati, E.C.V. / Saitta, F. / Drakou, C.E. / Leonidas, D.D. / Fessas, D. / Zographos, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bxuC ![]() 8bxvC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 14105.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: OBP-5 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 131 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/1BO.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/S5V.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1BO.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/S5V.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MPD / ( | ||||||
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#3: Chemical | ChemComp-1BO / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% ...Details: 0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→53.51 Å / Num. obs: 32113 / % possible obs: 97.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 7.5 / Num. unique obs: 4584 / CC1/2: 0.985 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.714 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.769 Å
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Refine LS restraints |
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LS refinement shell |
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