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Yorodumi- PDB-6ogh: Structure of Aedes aegypti OBP22 in the complex with linoleic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ogh | ||||||
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Title | Structure of Aedes aegypti OBP22 in the complex with linoleic 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 | 6ogh.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ogh.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ogh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/6ogh ftp://data.pdbj.org/pub/pdb/validation_reports/og/6ogh | HTTPS FTP |
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-Related structure data
Related structure data | 6nbnC 6og0C 6oiiC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14400.319 Da / Num. of mol.: 1 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, 156 molecules
#2: Chemical | #3: Chemical | ChemComp-CO / | #4: Chemical | ChemComp-EIC / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 40.09 % / 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, 4mM cadmium chloride, 4mM cobalt chloride, 4mM 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: Oct 15, 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→27.95 Å / Num. obs: 10076 / % possible obs: 99.92 % / Redundancy: 15.3 % / Biso Wilson estimate: 17.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0651 / Rpim(I) all: 0.01717 / Rrim(I) all: 0.06736 / Net I/σ(I): 45.41 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 14 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 28.57 / Num. unique obs: 987 / CC1/2: 0.998 / Rpim(I) all: 0.02926 / Rrim(I) all: 0.1101 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.455 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.116 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→28 Å
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Refine LS restraints |
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