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Yorodumi- PDB-8by4: Crystal structure of Odorant Binding Protein 1 from Aedes albopic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8by4 | |||||||||
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Title | Crystal structure of Odorant Binding Protein 1 from Aedes albopictus (Asian tiger mosquito) | |||||||||
Components | Odorant-binding protein 1 | |||||||||
Keywords | TRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction / Carvacrol | |||||||||
Function / homology | Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Odorant-binding protein 1 Function and homology information | |||||||||
Biological species | Aedes albopictus (Asian tiger mosquito) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Liggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E. | |||||||||
Funding support | Greece, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Odorant Binding Protein 1 from Aedes albopictus (Asian tiger mosquito) Authors: Liggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8by4.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8by4.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 8by4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/8by4 ftp://data.pdbj.org/pub/pdb/validation_reports/by/8by4 | HTTPS FTP |
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-Related structure data
Related structure data | 6og0S S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14190.069 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes albopictus (Asian tiger mosquito) Gene: 109422789, RP20_CCG014341, RP20_CCG027709 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A9Y0 |
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#2: 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: 4.3 Å3/Da / Density % sol: 71.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1.6M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.35 Å / Num. obs: 16836 / % possible obs: 99.96 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.65 / Num. unique obs: 1662 / CC1/2: 0.94 / % possible all: 99.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OG0 Resolution: 2→47.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.561 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.683 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.774 Å / Origin y: -26.389 Å / Origin z: 5.905 Å
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