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Yorodumi- PDB-4dxo: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dxo | |||||||||
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Title | Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X(6) | |||||||||
Components | LEA X(6) GFP-LIKE PROTEINS | |||||||||
Keywords | LUMINESCENT PROTEIN / BETA BARREL | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | |||||||||
Biological species | Synthetic Construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Kim, H. / Fromme, R. / Wachter, R.M. | |||||||||
Citation | Journal: Structure / Year: 2015 Title: A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Authors: Kim, H. / Zou, T. / Modi, C. / Dorner, K. / Grunkemeyer, T.J. / Chen, L. / Fromme, R. / Matz, M.V. / Ozkan, S.B. / Wachter, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dxo.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dxo.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 4dxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dxo_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 4dxo_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 4dxo_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4dxo_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dxo ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dxo | HTTPS FTP |
-Related 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: 26399.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic Construct (others) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-NA / |
#3: 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: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 0.07M tris, 0.2 M magnesium chloride, 16% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2009 |
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: 2.5→39.16 Å / Num. all: 8009 / Num. obs: 7913 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.1 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.681 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.314 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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