+Open data
-Basic information
Entry | Database: PDB / ID: 5dy6 | ||||||
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Title | Enhanced superfolder GFP with DBCO at 148 | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / click chemistry / non-canonical amino acids / superfolder GFP / DBCO-amine / chromophore / fluorecence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å | ||||||
Authors | Jones, D.D. / Rizkallah, P.J. / Worthy, H.L. | ||||||
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 | 5dy6.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dy6.ent.gz | 166.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/5dy6 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/5dy6 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 25940.150 Da / Num. of mol.: 2 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 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M PCTP Buffer, 15% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.66→72.18 Å / Num. obs: 14111 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Net I/σ(I): 15 / Num. measured all: 99142 | |||||||||||||||||||||||||||
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: 2.66→72.18 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2968 / WRfactor Rwork: 0.1918 / FOM work R set: 0.6265 / SU B: 63.073 / SU ML: 0.494 / SU R Cruickshank DPI: 0.3396 / SU Rfree: 0.4114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / 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: 204.03 Å2 / Biso mean: 111.809 Å2 / Biso min: 71.71 Å2
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Refinement step | Cycle: final / Resolution: 2.66→72.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.66→2.729 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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