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Yorodumi- PDB-6opb: Structure of Aedes aegypti OBP22 in the complex with arachidic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 6opb | ||||||
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Title | Structure of Aedes aegypti OBP22 in the complex with arachidic acid | ||||||
Components | AAEL005772-PA | ||||||
Keywords | TRANSPORT PROTEIN / Odorant binding protein / Chemo-sensory signaling / Lipid binding | ||||||
Function / homology | Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / lipid binding / icosanoic acid / Odorant binding protein Function and homology information | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6opb.cif.gz | 406.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6opb.ent.gz | 341.4 KB | Display | PDB format |
PDBx/mmJSON format | 6opb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6opb ftp://data.pdbj.org/pub/pdb/validation_reports/op/6opb | HTTPS FTP |
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-Related structure data
Related structure data | 6nbnC 6og0C 6oghC 6oiiC 6omwC 6otlC 6p2eC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14400.319 Da / Num. of mol.: 9 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 #2: Chemical | #3: Chemical | ChemComp-DMS / | #4: 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: 3.14 Å3/Da / Density % sol: 60.86 % / Description: hexagon stick |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 1.55M ammonium sulfate, 0.1M citric acid, 0.5M sodium 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: Aug 2, 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 twin |
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Reflection | Resolution: 2→38.56 Å / Num. obs: 102184 / % possible obs: 99.91 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04284 / Rpim(I) all: 0.02153 / Rrim(I) all: 0.04836 / Net I/σ(I): 30.17 | |||||||||||||||
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1576 / Mean I/σ(I) obs: 6.42 / Num. unique obs: 10406 / CC1/2: 0.916 / Rpim(I) all: 0.1356 / Rrim(I) all: 0.2089 / % possible all: 99.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: OBP22 structure slved by tantalum SAD Resolution: 2→38.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.006 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / 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: 28.715 Å2
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Refinement step | Cycle: 1 / Resolution: 2→38.56 Å
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Refine LS restraints |
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