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- PDB-1oxd: Expansion of the Genetic Code Enables Design of a Novel "Gold" Cl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oxd | ||||||
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Title | Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins | ||||||
![]() | cyan fluorescent protein cfp | ||||||
![]() | LUMINESCENT PROTEIN / green fluorescent protein / chromophore / amino acid incorporation / tryptophan / genetic code | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / : ![]() | ||||||
Biological species | cfp marker plasmid pWM1009 (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. ...Hyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N. | ||||||
![]() | ![]() Title: Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins Authors: Hyun Bae, J. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.2 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.9 KB | Display | ![]() |
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Full document | ![]() | 366 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25798.102 Da / Num. of mol.: 1 / Mutation: Q80R Source method: isolated from a genetically manipulated source Source: (gene. exp.) cfp marker plasmid pWM1009 (others) / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES 65THR, 66TRP AND 67GLY ARE MODIFIED TO MAKE THE CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 11, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→7.98 Å / Num. all: 79530 / Num. obs: 73514 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11 Å2 |
Reflection shell | Resolution: 1.15→1.22 Å / % possible all: 75.6 |
Reflection | *PLUS Lowest resolution: 8 Å / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS Lowest resolution: 1.17 Å / % possible obs: 84 % / Rmerge(I) obs: 0.247 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.4172 Å2 / ksol: 0.613 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.15→7.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.22 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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