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Yorodumi- PDB-8bvg: Bright fluorescent protein BrUSLEE with subnanosecond fluorescenc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bvg | ||||||
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Title | Bright fluorescent protein BrUSLEE with subnanosecond fluorescence lifetime | ||||||
Components | BrUSSLEE | ||||||
Keywords | FLUORESCENT PROTEIN / BrUSSLEE / GFP-like biomarker | ||||||
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: 2.38 Å | ||||||
Authors | Pletnev, V. / Pletneva, N. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Crystal Structure of Bright Fluorescent Protein BrUSLEE with Subnanosecond Fluorescence Lifetime; Electric and Dynamic Properties. Authors: Goryacheva, E. / Efremov, R. / Krylov, N. / Artemyev, I. / Bogdanov, A. / Mamontova, A. / Pletnev, S. / Pletneva, N. / Pletnev, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bvg.cif.gz | 276.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bvg.ent.gz | 230.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bvg ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bvg | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26765.217 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Six subunits in the crystal cell / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.42 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 6.4% Tacsimate pH 5.0, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.38→30 Å / Num. obs: 62234 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.998 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EGFP Resolution: 2.38→29.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.3919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.29 Å2 / Biso mean: 63.553 Å2 / Biso min: 29.61 Å2
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Refinement step | Cycle: final / Resolution: 2.38→29.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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