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Yorodumi- PDB-5fhv: Crystal structure of mCherry after reaction with 2-mercaptoethanol -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fhv | ||||||
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Title | Crystal structure of mCherry after reaction with 2-mercaptoethanol | ||||||
Components | mCherry-BME | ||||||
Keywords | FLUORESCENT PROTEIN / 2-mercaptoethanol / Michael addition | ||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / metal ion binding Similarity search - Function | ||||||
Biological species | Discosoma sp. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | De Zitter, E. / Dedecker, P. / Van Meervelt, L. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Efficient switching of mCherry fluorescence using chemical caging. Authors: Cloin, B.M.C. / De Zitter, E. / Salas, D. / Gielen, V. / Folkers, G.E. / Mikhaylova, M. / Bergeler, M. / Krajnik, B. / Harvey, J. / Hoogenraad, C.C. / Van Meervelt, L. / Dedecker, P. / Kapitein, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fhv.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fhv.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fhv ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fhv | HTTPS FTP |
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-Related structure data
Related structure data | 2h5qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30489.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): JM109 / References: UniProt: D0VWW2*PLUS | ||||
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#2: Chemical | ChemComp-PGE / | ||||
#3: Chemical | #4: Chemical | ChemComp-P6G / | #5: 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: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M MgCl2.6H2O, 0.1 M Tris pH 8.5, 25 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.55→45.381 Å / Num. obs: 34495 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H5Q Resolution: 1.55→45.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.86 Å2 / Biso mean: 17.7512 Å2 / Biso min: 5.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→45.381 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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