+Open data
-Basic information
Entry | Database: PDB / ID: 5jzk | ||||||
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Title | The Structure of Ultra Stable Green Fluorescent Protein | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / green fluorescent protein / GFP / thermostable | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yong, K.J. / Gunn, N.J. / Scott, D.J. / Griffin, M.D.W. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY. Authors: Scott, D.J. / Gunn, N.J. / Yong, K.J. / Wimmer, V.C. / Veldhuis, N.A. / Challis, L.M. / Haidar, M. / Petrou, S. / Bathgate, R.A.D. / Griffin, M.D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jzk.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jzk.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/5jzk ftp://data.pdbj.org/pub/pdb/validation_reports/jz/5jzk | HTTPS FTP |
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-Related structure data
Related structure data | 5jzlC 2b3pS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28107.637 Da / Num. of mol.: 2 / Fragment: UNP residues 3-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS |
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-Non-polymers , 5 types, 388 molecules
#2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 20 % w/v PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M Sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.22 Å / Num. obs: 41787 / % possible obs: 99.4 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rsym value: 0.097 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.9→49.22 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.647 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.954 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→49.22 Å
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Refine LS restraints |
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