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Yorodumi- PDB-6un5: Crystal structure of green fluorescent protein (GFP); S65T, Y66(2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6un5 | ||||||
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Title | Crystal structure of green fluorescent protein (GFP); S65T, Y66(2,3,5-F3Y); ih circular permutant (50-51) | ||||||
Components | Green fluorescent protein,Green fluorescent protein | ||||||
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 / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Lin, C.-Y. / 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 | 6un5.cif.gz | 207.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6un5.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 6un5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/6un5 ftp://data.pdbj.org/pub/pdb/validation_reports/un/6un5 | HTTPS FTP |
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-Related structure data
Related structure data | 6og8C 6og9C 6ogaC 6ogbC 6ogcC 6un6C 6un7C 6ofkS 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: 28268.502 Da / Num. of mol.: 2 Mutation: A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V, S232R, Y241I, C250S,A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp, GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059PIQ0, UniProt: P42212 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.74 Å3/Da / Density % sol: 29.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 31% PEG 3350 |
-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: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.358→38.929 Å / Num. obs: 81547 / % possible obs: 98.2 % / Redundancy: 13.36 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.13 |
Reflection shell | Resolution: 1.36→1.4 Å / Redundancy: 13.23 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 5968 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OFK Resolution: 1.36→38.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→38.93 Å
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LS refinement shell |
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