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Yorodumi- PDB-4kag: Crystal structure analysis of a single amino acid deletion mutati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kag | ||||||
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Title | Crystal structure analysis of a single amino acid deletion mutation in EGFP | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel / chromophore cyclisation / single amino acid deletion mutation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å | ||||||
Authors | Arpino, J.A.J. / Rizkallah, P.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. Authors: Arpino, J.A. / Rizkallah, P.J. / Jones, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kag.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kag.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/4kag ftp://data.pdbj.org/pub/pdb/validation_reports/ka/4kag | HTTPS FTP |
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-Related structure data
Related structure data | 4kexC 4eulS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26841.355 Da / Num. of mol.: 1 / Mutation: F64L, S65T, D190delta Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pNOM-XP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P42212 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M Na cacodylate, 0.2 M NaCl, 1M Na citrate, pH 6.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→39.94 Å / Num. obs: 91397 / % possible obs: 97.3 % / Redundancy: 9.1 % |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4EUL Resolution: 1.12→39.94 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.0292 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→39.94 Å
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Refine LS restraints |
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