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Yorodumi- PDB-1oxf: Expansion of the Genetic Code Enables Design of a Novel "Gold" Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oxf | |||||||||
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Title | Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins | |||||||||
Components | cyan fluorescent protein cfp | |||||||||
Keywords | LUMINESCENT PROTEIN / green fluorescent protein / chromophore / amino acid incorporation / tryptophan / genetic code | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / : Function and homology information | |||||||||
Biological species | cfp marker plasmid pWM1009 (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
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. ...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. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oxf.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oxf.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oxf_validation.pdf.gz | 373.6 KB | Display | wwPDB validaton report |
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Full document | 1oxf_full_validation.pdf.gz | 376.8 KB | Display | |
Data in XML | 1oxf_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1oxf_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/1oxf ftp://data.pdbj.org/pub/pdb/validation_reports/ox/1oxf | HTTPS FTP |
-Related 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: 25554.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) cfp marker plasmid pWM1009 (others) / Production host: Escherichia coli (E. coli) / References: GenBank: 11321072 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % | ||||||||||||||||||||||||||||||||||||
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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 25K | ||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
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: 1.64→7.99 Å / Num. all: 26932 / Num. obs: 24503 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.2 Å2 |
Reflection shell | Resolution: 1.64→1.74 Å / % possible all: 81.9 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 10 Å / % possible obs: 89.9 % / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.224 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→7.99 Å / Rfactor Rfree error: 0.005 / 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: 64.0105 Å2 / ksol: 0.506258 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.69→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.74 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.226 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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