+Open data
-Basic information
Entry | Database: PDB / ID: 8arm | ||||||
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Title | Crystal structure of LSSmScarlet2 | ||||||
Components | LSSmScarlet2 | ||||||
Keywords | FLUORESCENT PROTEIN / LSSmScarlet2 | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Red fluorescent protein drFP583 Function and homology information | ||||||
Biological species | Discosoma sp. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Samygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Subach, F.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: LSSmScarlet2 and LSSmScarlet3, Chemically Stable Genetically Encoded Red Fluorescent Proteins with a Large Stokes' Shift. Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Piatkevich, K.D. / Patrushev, M.V. / Samygina, V.R. / Subach, F.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8arm.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8arm.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 8arm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/8arm ftp://data.pdbj.org/pub/pdb/validation_reports/ar/8arm | HTTPS FTP |
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-Related structure data
Related structure data | 5lk4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 26513.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, MES pH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.967697 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967697 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→39.8 Å / Num. obs: 42307 / % possible obs: 97.57 % / Redundancy: 1.56 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 1 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.41→1.45 Å / Mean I/σ(I) obs: 4.43 / Num. unique obs: 2725 / CC1/2: 0.94 / Rrim(I) all: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LK4 Resolution: 1.41→15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.713 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.053 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: 12.017 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→15 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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