+Open data
-Basic information
Entry | Database: PDB / ID: 5oxb | ||||||
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Title | Structure of blue-light irradiated Cerulean | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / tryptophan-based chromophore / Cerulean / photoisomerization | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Gotthard, G. / von Stetten, D. / Clavel, D. / Noirclerc-Savoye, M. / Royant, A. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Chromophore Isomer Stabilization Is Critical to the Efficient Fluorescence of Cyan Fluorescent Proteins. Authors: Gotthard, G. / von Stetten, D. / Clavel, D. / Noirclerc-Savoye, M. / Royant, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oxb.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxb.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxb ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxb | HTTPS FTP |
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-Related structure data
Related structure data | 5ox8C 5ox9C 5oxaC 5oxcC 2wsoS S: Starting model for refinement C: citing same article (ref.) |
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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: 26791.252 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66W, N146I, H148D, M153T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pQE-60 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P42212 |
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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: 2.2 Å3/Da / Density % sol: 44.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES pH 7.0, 12% PEG8000, 100mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953725 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953725 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→46.48 Å / Num. obs: 46320 / % possible obs: 100 % / Redundancy: 7.07 % / Rrim(I) all: 0.054 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 6.94 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 10097 / Rrim(I) all: 0.883 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WSO Resolution: 1.38→46.48 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.955 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.051 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.093 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→46.48 Å
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Refine LS restraints |
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