+Open data
-Basic information
Entry | Database: PDB / ID: 6mtf | ||||||
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Title | D7 protein from Phlebotomus duboscqi, native | ||||||
Components | 26.7 kDa salivary protein | ||||||
Keywords | TRANSPORT PROTEIN / sand fly / odorant-binding protein / leukotriene / thromboxane / salivary | ||||||
Function / homology | Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / 26.7 kDa salivary protein Function and homology information | ||||||
Biological species | Phlebotomus duboscqi (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å | ||||||
Authors | Andersen, J.F. / Jablonka, W. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Functional and structural similarities of D7 proteins in the independently-evolved salivary secretions of sand flies and mosquitoes. Authors: Jablonka, W. / Kim, I.H. / Alvarenga, P.H. / Valenzuela, J.G. / Ribeiro, J.M.C. / Andersen, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mtf.cif.gz | 200.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mtf.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mtf ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mtf | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 26825.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phlebotomus duboscqi (insect) / Gene: M01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q06KA2 #2: Chemical | #3: 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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 6000, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→41.487 Å / Num. obs: 38751 / % possible obs: 99.9 % / Redundancy: 11.85 % / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.92→1.96 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.33 / Num. unique obs: 2811 / CC1/2: 0.927 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→41.487 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 18.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.34 Å2 / Biso mean: 18.534 Å2 / Biso min: 5.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→41.487 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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