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Yorodumi- PDB-4r6b: Rational Design of Enhanced Photoresistance in a Photoswitchable ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r6b | |||||||||
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Title | Rational Design of Enhanced Photoresistance in a Photoswitchable Fluorescent Protein | |||||||||
Components | Green to red photoconvertible GFP-like protein EosFP | |||||||||
Keywords | FLUORESCENT PROTEIN / Beta-barrel | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Lobophyllia hemprichii (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Duan, C. / Adam, V. / Byrdin, M. / Bourgeois, D. | |||||||||
Citation | Journal: Methods Appl Fluoresc / Year: 2015 Title: Rational design of enhanced photoresistance in a photoswitchable fluorescent protein. Authors: Duan, C. / Byrdin, M. / El Khatib, M. / Henry, X. / Adam, V. / Bourgeois, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r6b.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r6b.ent.gz | 164.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6b ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6b | HTTPS FTP |
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-Related structure data
Related structure data | 2vvhS 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: 26481.906 Da / Num. of mol.: 4 / Mutation: M159A, F173S, F191L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5S6Z9 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SO3 / #4: 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: 2.75 Å3/Da / Density % sol: 55.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 2.1M ammonium sulfate, 0.1M Bicine, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013 / Details: Toroidal focusing mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93928 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.11 Å / Num. all: 81761 / Num. obs: 78818 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 29.18 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.64 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4684 / Mean I/σ(I) obs: 3 / Num. unique all: 7644 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2VVH Resolution: 2→42.11 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 24.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.11 Å
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Refine LS restraints |
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LS refinement shell |
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