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Yorodumi- PDB-1s6z: Enhanced Green Fluorescent Protein Containing the Y66L Substitution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6z | ||||||
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Title | Enhanced Green Fluorescent Protein Containing the Y66L Substitution | ||||||
Components | green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / Chromophore / Eleven-stranded Beta Barrel / Trapped Intermediate / Backbone cyclization / GFP-like Protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Rosenow, M.A. / Huffman, H.A. / Phail, M.E. / Wachter, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: The Crystal Structure of the Y66L Variant of Green Fluorescent Protein Supports a Cyclization-Oxidation-Dehydration Mechanism for Chromophore Maturation(,). Authors: Rosenow, M.A. / Huffman, H.A. / Phail, M.E. / Wachter, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6z.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6z.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6z ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6z | HTTPS FTP |
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-Related structure data
Related structure data | 1emaS 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: 26863.367 Da / Num. of mol.: 1 / Mutation: F64L/S65T/Y66L Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): JM109-DE3 / References: GenBank: 1842445, UniProt: P42212*PLUS |
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#2: Chemical | ChemComp-CL / |
#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: 2.18 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, calcium acetate, cacodylate, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 20, 2003 / Details: osmic confocal mirrors |
Radiation | Monochromator: osmic confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 35186 / Num. obs: 35157 / % possible obs: 96.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 5.9 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 1.5→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1191346.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 10000 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.7283 Å2 / ksol: 0.44157 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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