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Yorodumi- PDB-2gx0: Crystal structural and functional analysis of GFP-like fluorescen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gx0 | |||||||||
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Title | Crystal structural and functional analysis of GFP-like fluorescent protein | |||||||||
Components | fluorescent protein DronpaFluorescence | |||||||||
Keywords | LUMINESCENT PROTEIN / fluorescence / b-can / photoswitching | |||||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Echinophyllia sp. SC22 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Hwang, K.Y. / Nam, K.-H. / Park, S.-Y. / Sugiyama, K. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: Structural characterization of the photoswitchable fluorescent protein Dronpa-C62S Authors: Nam, K.-H. / Kwon, O.Y. / Sugiyama, K. / Lee, W.-H. / Kim, Y.K. / Song, H.K. / Kim, E.E. / Park, S.-Y. / Jeon, H. / Hwang, K.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gx0.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gx0.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/2gx0 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/2gx0 | HTTPS FTP |
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-Related structure data
Related structure data | 2gx2C 1xssS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27613.295 Da / Num. of mol.: 4 / Fragment: Green fluorescent protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5TLG6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 68388 / Num. obs: 68388 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.6 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 66.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XSS Resolution: 1.9→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 89612.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.9079 Å2 / ksol: 0.34058 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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