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Yorodumi- PDB-6og9: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6og9 | ||||||
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Title | Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51) | ||||||
Components | Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; 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: 1.798 Å | ||||||
Authors | Lin, C.-Y. / Deng, A. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Phys.Chem.B / Year: 2020 Title: Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. Authors: Lin, C.Y. / 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 | 6og9.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6og9.ent.gz | 168.2 KB | Display | PDB format |
PDBx/mmJSON format | 6og9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/6og9 ftp://data.pdbj.org/pub/pdb/validation_reports/og/6og9 | HTTPS FTP |
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-Related structure data
Related structure data | 6og8C 6ogaC 6ogbC 6ogcC 6un5C 6un6C 6un7C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28096.254 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: 1.9 Å3/Da / Density % sol: 35.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM sodium acetate, pH 5.0, 100 mM NaCl, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→36.594 Å / Num. obs: 38844 / % possible obs: 98.78 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1052 / Rpim(I) all: 0.06394 / Rrim(I) all: 0.1234 / Net I/σ(I): 12.58 |
Reflection shell | Resolution: 1.798→1.863 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.7413 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 3808 / CC1/2: 0.644 / Rpim(I) all: 0.4528 / Rrim(I) all: 0.8709 / % possible all: 97.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4zf3 Resolution: 1.798→36.594 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→36.594 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.3154 Å / Origin y: -0.4268 Å / Origin z: 76.4031 Å
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Refinement TLS group | Selection details: all |