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Yorodumi- PDB-6ofo: Crystal structure of split green fluorescent protein (GFP); s10 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ofo | |||||||||
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Title | Crystal structure of split green fluorescent protein (GFP); s10 circular permutant (194-195) | |||||||||
Components | Green fluorescent protein (GFP); s10 circular permutant (194-195) | |||||||||
Keywords | FLUORESCENT PROTEIN / GFP / SPLIT FLUORESCENT PROTEIN | |||||||||
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: 2.603 Å | |||||||||
Authors | Lin, C.-Y. / Romei, M.G. / Deller, M.C. / Doukov, T.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 | 6ofo.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofo.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ofo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofo ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofo | HTTPS FTP |
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-Related structure data
Related structure data | 6ofkC 6oflC 6ofmC 6ofnC 2b3pS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28216.389 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: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 20% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.043 Å / Num. obs: 14682 / % possible obs: 92.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.192 / Net I/σ(I): 6.43 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1109 / CC1/2: 0.553 / Rrim(I) all: 1.79 / % possible all: 71.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2b3p Resolution: 2.603→39.043 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→39.043 Å
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Refine LS restraints |
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LS refinement shell |
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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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