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Yorodumi- PDB-6pfu: rsEGFP2 with a chlorinated chromophore in the non-fluorescent off... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pfu | |||||||||
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Title | rsEGFP2 with a chlorinated chromophore in the non-fluorescent off-state in a contracted unit cell | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN / Green 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: 1.619 Å | |||||||||
Authors | Chang, J. / Romei, M.G. / Boxer, S.G. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins. Authors: Chang, J. / Romei, M.G. / 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 | 6pfu.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pfu.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/6pfu ftp://data.pdbj.org/pub/pdb/validation_reports/pf/6pfu | HTTPS FTP |
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-Related structure data
Related structure data | 6pfrC 6pfsC 6pftC 5dtyS 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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Unit cell |
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-Components
#1: Protein | Mass: 28566.648 Da / Num. of mol.: 1 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 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 1.76 M ammonium sulfate, 0.1 M HEPES; Cryoprotectant 1.6 M sucrose, 2.72 M ammonium sulfate, 0.16 M HEPES. Temp details: Room temp |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.619→38.86 Å / Num. obs: 25996 / % possible obs: 99.38 % / Redundancy: 2 % / Biso Wilson estimate: 20.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02333 / Rrim(I) all: 0.03299 / Net I/σ(I): 14.19 |
Reflection shell | Resolution: 1.619→1.677 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4409 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2533 / CC1/2: 1 / Rrim(I) all: 0.6235 / % possible all: 98.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DTY Resolution: 1.619→38.856 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.619→38.856 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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