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Open data
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Basic information
Entry | Database: PDB / ID: 6e6o | ||||||
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Title | Pheromone from Euplotes raikovi, Er-1 | ||||||
![]() | Mating pheromone Er-1/Er-3 | ||||||
![]() | SIGNALING PROTEIN / PHEROMONE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Finke, A.D. / Marsh, M.E. | ||||||
![]() | ![]() Title: Ab initio crystal structure determination of Euplotes raikovi pheromones from high-resolution data Authors: Finke, A.D. / Pedrini, B. / Alimenti, C. / Vallesi, A. / Luporini, P. / Marsh, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26 KB | Display | ![]() |
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PDB format | ![]() | 19.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 416.2 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 4417.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.47 Å3/Da / Density % sol: 16.31 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 0.1 M to 0.2 M (NH4)2SO4, 0.05 M Na Citrate pH 3.5 and 6% (v/v) ethanol, using 5-ul protein drops and 5 ul of reservoir solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6192 Å / Relative weight: 1 |
Reflection | Resolution: 0.7→25.02 Å / Num. obs: 39777 / % possible obs: 97 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09503 / Net I/σ(I): 9.41 |
Reflection shell | Resolution: 0.7→0.725 Å / Rmerge(I) obs: 1.63 / CC1/2: 0.447 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.7→25.02 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.43 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.895 Å2
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Refinement step | Cycle: 1 / Resolution: 0.7→25.02 Å
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Refine LS restraints |
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