+Open data
-Basic information
Entry | Database: PDB / ID: 7a7r | ||||||
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Title | rsGreenF-K206A in the green-off state | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / Reversible photoswitchable fluorescent protein | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DI(HYDROXYETHYL)ETHER / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | De Zitter, E. / Dedecker, P. / Van Meervelt, L. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*. Authors: De Zitter, E. / Hugelier, S. / Duwe, S. / Vandenberg, W. / Tebo, A.G. / Van Meervelt, L. / Dedecker, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a7r.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a7r.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 7a7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/7a7r ftp://data.pdbj.org/pub/pdb/validation_reports/a7/7a7r | HTTPS FTP |
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-Related structure data
Related structure data | 7a7kC 7a7lC 7a7mC 7a7nC 7a7oC 7a7pC 7a7qC 7a7sC 7a7tC 7a7uC 7a7vC 7a7wC 7a7xC 7a7yC 7a7zC 7a80C 7a81C 7a82C 7a83C 7a84C 7a85C 7a86C 7a87C 7a88C 7a89C 7a8aC 7a8bC 7a8cC 7a8dC 7a8eC 7a8fC 7a8gC 7a8hC 7a8iC 7a8jC 7a8kC 7a8lC 7a8mC 7a8nC 7a8oC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30614.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / Variant (production host): JM109 / References: UniProt: A0A059PIQ0 |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM NaCl 100 mM MES pH 6.0 20 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→47.49 Å / Num. obs: 9057 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 25.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.043 / Rrim(I) all: 0.152 / Net I/σ(I): 16.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→47.487 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.15 / 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: 91.44 Å2 / Biso mean: 25.328 Å2 / Biso min: 3.55 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→47.487 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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