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Yorodumi- PDB-6ofl: Crystal structure of green fluorescent protein (GFP); S65T, Y66(3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ofl | ||||||
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Title | Crystal structure of green fluorescent protein (GFP); S65T, Y66(3-ClY); ih circular permutant (50-51) | ||||||
Components | Green fluorescent protein (GFP); S65T, Y66(3-ClY); ih circular permutant (50-51) | ||||||
Keywords | FLUORESCENT PROTEIN / GFP | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Lin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. Authors: Lin, C.Y. / Romei, M.G. / Oltrogge, L.M. / Mathews, I.I. / Boxer, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ofl.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofl.ent.gz | 183 KB | Display | PDB format |
PDBx/mmJSON format | 6ofl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofl ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofl | HTTPS FTP |
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-Related structure data
Related structure data | 6ofkC 6ofmC 6ofnC 6ofoC 4zf3S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 28117.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS #2: 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: 1.91 Å3/Da / Density % sol: 35.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.15 M ammonium acetate, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→36.52 Å / Num. obs: 113139 / % possible obs: 96.9 % / Redundancy: 23 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 1 / Rrim(I) all: 0.058 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7995 / CC1/2: 0.721 / Rrim(I) all: 1.65 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4zf3 Resolution: 1.25→36.52 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.766 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→36.52 Å
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Refine LS restraints |
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