+Open data
-Basic information
Entry | Database: PDB / ID: 6e6n | ||||||
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Title | Pheromone from Euplotes raikovi, Er-13 | ||||||
Components | Pheromone from Euplotes raikovi Er-13 | ||||||
Keywords | SIGNALING PROTEIN / PHEROMONE | ||||||
Function / homology | Pheromone, protozoan / Euplotes raikovi mating pheromone / Er-13 prepro-pheromone Function and homology information | ||||||
Biological species | Euplotes raikovi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.363 Å | ||||||
Authors | Finke, A.D. / Marsh, M.E. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e6n.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e6n.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 6e6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e6n ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e6n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4056.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euplotes raikovi (eukaryote) / References: UniProt: A0A482LMF4*PLUS |
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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: 1.83 Å3/Da / Density % sol: 32.92 % |
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Crystal grow | Temperature: 293 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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.6198 Å |
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: 0.6198 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→39.12 Å / Num. obs: 85988 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.0524 / Net I/σ(I): 9.41 |
Reflection shell | Resolution: 1.363→1.411 Å / Rmerge(I) obs: 0.8927 / CC1/2: 0.9315 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.363→39.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.256 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.775 Å2
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Refinement step | Cycle: 1 / Resolution: 1.363→39.12 Å
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Refine LS restraints |
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