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Yorodumi- PDB-6d38: Photodissociable dimeric Dronpa green fluorescent protein variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d38 | |||||||||
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Title | Photodissociable dimeric Dronpa green fluorescent protein variant M (pdDronpaM) | |||||||||
Components | Fluorescent protein DronpaFluorescence | |||||||||
Keywords | FLUORESCENT PROTEIN / Dronpa / pdDronpa / Optogenetics / GFP / dimer / photodissociable | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding / Fluorescent protein Dronpa Function and homology information | |||||||||
Biological species | Echinophyllia sp. SC22 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Zhou, X. / Fan, L. / Lin, M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2017 Title: Optical control of cell signaling by single-chain photoswitchable kinases. Authors: Zhou, X.X. / Fan, L.Z. / Li, P. / Shen, K. / Lin, M.Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d38.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d38.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 6d38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/6d38 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/6d38 | HTTPS FTP |
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-Related structure data
Related structure data | 6d39C 2z6yS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29773.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLG6 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH) Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 6120 / % possible obs: 99.4 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2 / Num. unique obs: 290 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6Y Resolution: 2.8→43.909 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→43.909 Å
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Refine LS restraints |
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LS refinement shell |
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