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Yorodumi- PDB-2z6x: Crystal structure of 22G, the wild-type protein of the photoswitc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6x | |||||||||
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Title | Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein Dronpa | |||||||||
Components | photochromic protein DronpaPhotochromism | |||||||||
Keywords | FLUORESCENT PROTEIN / GFP-like Protein / Dronpa | |||||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pectiniidae (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 2z6x.cif.gz | 371.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6x.ent.gz | 303 KB | Display | PDB format |
PDBx/mmJSON format | 2z6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6x ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6x | HTTPS FTP |
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-Related structure data
Related structure data | 2z1oC 2z6yC 2z6zC 1ggxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29230.107 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectiniidae (invertebrata) / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q5TLG6*PLUS #2: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE RESIDUES (-32)-0 ARE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE RESIDUES (-32)-0 ARE EXPRESSION | |
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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: 2.09 Å3/Da / Density % sol: 41.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium dihydrogen phosphate, 40 % MPD, 0.1M Tris-HCl (pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-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: May 19, 2005 |
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: 2.3→50 Å / Num. all: 85028 / Num. obs: 85028 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 5.3 / Num. unique all: 8470 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GGX Resolution: 2.3→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 327000.99 / 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: 37.1246 Å2 / ksol: 0.28926 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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