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Yorodumi- PDB-5btt: Switching GFP fluorescence using genetically encoded phenyl azide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5btt | ||||||
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Title | Switching GFP fluorescence using genetically encoded phenyl azide chemistry through two different non-native post-translational modifications routes at the same position. | ||||||
Components | (Green fluorescent protein) x 2 | ||||||
Keywords | FLUORESCENT PROTEIN / synthetic biology / photocontrol / optogenetics / unnatural amino acids / protein fluorescence / sfGFP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å | ||||||
Authors | Hartley, A.M. / Worthy, H.L. / Reddington, S.C. / Rizkallah, P.J. / Jones, D.D. | ||||||
Citation | Journal: Chem Sci / Year: 2016 Title: Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle. Authors: Hartley, A.M. / Worthy, H.L. / Reddington, S.C. / Rizkallah, P.J. / Jones, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5btt.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5btt.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 5btt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/5btt ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5btt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 25854.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0 | ||||
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#2: Protein | Mass: 25854.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0 | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 3.09 Å3/Da / Density % sol: 60.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 50 mM MMT, 2.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 13, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.14→56.24 Å / Num. obs: 36124 / % possible obs: 100 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.022 / Net I/σ(I): 22.9 / Num. measured all: 525718 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→56.24 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.737 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.41 Å2 / Biso mean: 42.408 Å2 / Biso min: 22.8 Å2
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Refinement step | Cycle: final / Resolution: 2.14→56.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.14→2.196 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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