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Yorodumi- PDB-6oii: Structure of Aedes aegypti OBP22 in the complex with arachidonic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oii | ||||||
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Title | Structure of Aedes aegypti OBP22 in the complex with arachidonic acid | ||||||
Components | AAEL005772-PA | ||||||
Keywords | TRANSPORT PROTEIN / Odorant binding protein / Chemo-sensory signaling / Lipid binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.85 Å | ||||||
Authors | Jones, D.N. / Wang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail. Authors: Wang, J. / Murphy, E.J. / Nix, J.C. / Jones, D.N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oii.cif.gz | 201.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oii.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 6oii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oii ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oii | HTTPS FTP |
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-Related structure data
Related structure data | 6nbnC 6og0C 6oghC 6omwC 6opbC 6otlC 6p2eC C: citing same article (ref.) |
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Similar structure data |
-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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14400.319 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Tissue: Antennal cDNA / Gene: 5567053, AAEL005772 / Plasmid: pET13a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1HRL7 |
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-Non-polymers , 5 types, 187 molecules
#2: Chemical | ChemComp-EDO / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.65 % / Description: plate |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350 12 w/v, 0.1M sodium HEPES, 10mM cadmium chloride, 6mM cobalt chloride, 6mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS3 X 200K-A / Detector: PIXEL / Date: Nov 7, 2018 / Details: VariMax Cu-HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→27.9 Å / Num. obs: 19395 / % possible obs: 99.41 % / Redundancy: 14.6 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.02954 / Rrim(I) all: 0.114 / Net I/σ(I): 17.88 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.7619 / Mean I/σ(I) obs: 4.15 / Num. unique obs: 1900 / CC1/2: 0.929 / Rpim(I) all: 0.2127 / Rrim(I) all: 0.7922 / % possible all: 99.01 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→27.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.762 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.357 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→27.9 Å
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Refine LS restraints |
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