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Yorodumi- PDB-1myw: CRYSTAL STRUCTURE OF A YELLOW FLUORESCENT PROTEIN WITH IMPROVED M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1myw | ||||||
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Title | CRYSTAL STRUCTURE OF A YELLOW FLUORESCENT PROTEIN WITH IMPROVED MATURATION AND REDUCED ENVIRONMENTAL SENSITIVITY | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / GREEN FLUORESCENT PROTEIN / YELLOW-EMISSION VARIANT / IMPROVED MATURATION / BETA-BARREL / CHROMOPHORE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Rekas, A. / Alattia, J.R. / Nagai, T. / Miyawaki, A. / Ikura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of Venus, a Yellow Fluorescent Protein with Improved Maturation and Reduced Environmental Sensitivity Authors: Rekas, A. / Alattia, J.R. / Nagai, T. / Miyawaki, A. / Ikura, M. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES GLY65, TYR66, AND GLY67 ARE NOT PRESENT IN THE ENTRY. INSTEAD THEY ARE REPLACED WITH CR266. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1myw.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1myw.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 1myw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1myw_validation.pdf.gz | 374.2 KB | Display | wwPDB validaton report |
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Full document | 1myw_full_validation.pdf.gz | 377.8 KB | Display | |
Data in XML | 1myw_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1myw_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/1myw ftp://data.pdbj.org/pub/pdb/validation_reports/my/1myw | HTTPS FTP |
-Related structure data
Related structure data | 1yfpS 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: 26875.287 Da / Num. of mol.: 1 / Fragment: residues 2-230 Mutation: F46L, F64L, S65G, V68L, S72A, M153T, V163A, S175G, T203Y Source method: isolated from a genetically manipulated source Details: SEYFP-F46L variant / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: PRSET_B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212 |
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#2: 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: 2.65 Å3/Da / Density % sol: 53.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: Tris, ammonium sulfate, PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.88 Å / Num. all: 14560 / Num. obs: 14560 / % possible obs: 97.7 % / Redundancy: 8.34 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.2→2.34 Å / Rmerge(I) obs: 0.317 / % possible all: 94.5 |
Reflection | *PLUS Num. obs: 121451 |
Reflection shell | *PLUS Highest resolution: 2.28 Å / Lowest resolution: 2.37 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFP Resolution: 2.2→23.88 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.5482 Å2 / ksol: 0.412254 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.13 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→23.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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