+Open data
-Basic information
Entry | Database: PDB / ID: 8ovy | ||||||
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Title | Structure of analogue of superfolded GFP | ||||||
Components | Green fluorescent protein | ||||||
Keywords | TRANSLATION | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.537 Å | ||||||
Authors | Dunkelmann, D. / Fiedler, M. / Bellini, D. / Alvira, C.P. / Chin, J.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2024 Title: Adding alpha , alpha-disubstituted and beta-linked monomers to the genetic code of an organism. Authors: Dunkelmann, D.L. / Piedrafita, C. / Dickson, A. / Liu, K.C. / Elliott, T.S. / Fiedler, M. / Bellini, D. / Zhou, A. / Cervettini, D. / Chin, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ovy.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ovy.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ovy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/8ovy ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovy | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27983.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.93 Å3/Da / Density % sol: 36.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, Bicine/Trizma 0.1 M pH 8.5, Morpheus III Alkaloids 0.8% w/v, Morpheus Alcohols 0.12 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.84 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.537→88.071 Å / Num. obs: 59575 / % possible obs: 93.1 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rrim(I) all: 0.11 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.537→1.595 Å / Num. unique obs: 5803 / CC1/2: 0.34 / Rrim(I) all: 1.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.537→88.071 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.218 / SU B: 1.74 / SU ML: 0.062 / Average fsc free: 0.9124 / Average fsc work: 0.9236 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.089 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.863 Å2
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Refinement step | Cycle: LAST / Resolution: 1.537→88.071 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: 20
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