+Open data
-Basic information
Entry | Database: PDB / ID: 7a8k | ||||||
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Title | rsGreen0.7-K206A-H148V partially 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 / molecular replacement / Resolution: 2.25 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 | 7a8k.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a8k.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 7a8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a8k_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 7a8k_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 7a8k_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7a8k_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/7a8k ftp://data.pdbj.org/pub/pdb/validation_reports/a8/7a8k | HTTPS FTP |
-Related structure data
Related structure data | 7a7kC 7a7lC 7a7mC 7a7nC 7a7oC 7a7pC 7a7qC 7a7rC 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 7a8lC 7a8mC 7a8nC 7a8oC 4xowS 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: 30572.322 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: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 7.5 12 % PEG 4000 1% tryptone |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2016 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→42.13 Å / Num. obs: 11804 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Rrim(I) all: 0.088 / Net I/σ(I): 10 / Num. measured all: 43972 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 4XOW Resolution: 2.25→39.299 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.31 Å2 / Biso mean: 50.4816 Å2 / Biso min: 26.41 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→39.299 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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