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Yorodumi- PDB-2z6y: Crystal structure of a photoswitchable GFP-like protein Dronpa in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6y | |||||||||
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Title | Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state | |||||||||
Components | Fluorescent protein Dronpa | |||||||||
Keywords | FLUORESCENT PROTEIN / GFP-like Protein / photochromism | |||||||||
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: 2 Å | |||||||||
Authors | Kikuchi, A. / Jeyakanthan, J. / Taka, J. / Shiro, Y. / Mizuno, H. / Miyawaki, A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. Authors: Mizuno, H. / Mal, T.K. / Walchli, M. / Kikuchi, A. / Fukano, T. / Ando, R. / Jeyakanthan, J. / Taka, J. / Shiro, Y. / Ikura, M. / Miyawaki, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6y.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6y.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 2z6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6y_validation.pdf.gz | 398.6 KB | Display | wwPDB validaton report |
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Full document | 2z6y_full_validation.pdf.gz | 416.8 KB | Display | |
Data in XML | 2z6y_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 2z6y_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6y ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6y | HTTPS FTP |
-Related structure data
Related structure data | 2z1oC 2z6xC 2z6zSC 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: 25780.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q5TLG6 #2: Water | ChemComp-HOH / | Sequence details | THE RESIDUE 63 IN THIS SEQUENCE IS GYC, CHROMOPHOR | |
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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: 1.98 Å3/Da / Density % sol: 37.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3000, 0.2M Ca(acetate)2, 0.1M Tris/HCl (pH 7.0), VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 27, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 53536 / Num. obs: 53536 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.118 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.1 / Num. unique all: 5274 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6Z Resolution: 2→19.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 273550.59 / 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: 34.2569 Å2 / ksol: 0.327402 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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