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Yorodumi- PDB-4zf4: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zf4 | ||||||
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Title | Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(Cl1Y), H148D; circular permutant (50-51) | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.823 Å | ||||||
Authors | Oltrogge, L.M. / Boxer, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2015 Title: Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP). Authors: Oltrogge, L.M. / 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 | 4zf4.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zf4.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/4zf4 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/4zf4 | HTTPS FTP |
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-Related structure data
Related structure data | 4zf3C 4zf5C 2dufS C: citing same article (ref.) S: Starting model for refinement |
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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: 28225.916 Da / Num. of mol.: 2 Mutation: S30R, Y39I, C48S, F64L, S65T, Q80R, F99S, N105K, E111V, I128T, Y145F, H148D, M153T, V163A, K166T, I167V, I171V, S205T, A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212 #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: 1.89 Å3/Da / Density % sol: 34.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM sodium acetate, 100 mM NaCl, 15% (wt/vol) PEG 3550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.344 Å / Num. obs: 37043 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.67 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DUF Resolution: 1.823→36.344 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.55 Å2 / Biso mean: 22.7147 Å2 / Biso min: 11.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.823→36.344 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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