+Open data
-Basic information
Entry | Database: PDB / ID: 4jfg | |||||||||
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Title | Crystal structure of sfGFP-66-HqAla | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | LUMINESCENT PROTEIN / 11-stranded beta-barrel | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.001 Å | |||||||||
Authors | Wang, J. / Liu, X. / Li, J. / Zhang, W. / Hu, M. / Zhou, J. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: Significant expansion of the fluorescent protein chromophore through the genetic incorporation of a metal-chelating unnatural amino acid. Authors: Liu, X. / Li, J. / Hu, C. / Zhou, Q. / Zhang, W. / Hu, M. / Zhou, J. / Wang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jfg.cif.gz | 683.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jfg.ent.gz | 565.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/4jfg ftp://data.pdbj.org/pub/pdb/validation_reports/jf/4jfg | HTTPS FTP |
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-Related structure data
Related structure data | 2b3pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27680.113 Da / Num. of mol.: 8 Mutation: S30R, Y39N, Q80R, F99S, N105T, Y145F, M153T, V163A, I171V, A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 #2: Chemical | ChemComp-HQY / #3: Chemical | ChemComp-CS / #4: 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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15-20% polyethylene glycol (PEG) 3350, 0.13-0.18M CsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIHAKU Satun944HG / Detector: CCD / Date: Feb 3, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 36392 / % possible obs: 84.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 3.001→21.841 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 32.52 / 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 |
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Refinement step | Cycle: LAST / Resolution: 3.001→21.841 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: -21.4139 Å / Origin y: -49.993 Å / Origin z: -57.6708 Å
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Refinement TLS group | Selection details: ALL |