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- PDB-3bxa: Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 4.2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bxa | ||||||
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Title | Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 4.2 | ||||||
![]() | Far-red fluorescent protein mKate | ||||||
![]() | FLUORESCENT PROTEIN / Far-red fluorescent protein / E. quadricolor / Chromophore structure / pH-induced cis-trans izomerization | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / CITRIC ACID![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pletnev, S. / Pletneva, N. / Pletnev, V. | ||||||
![]() | ![]() Title: A Crystallographic Study of Bright Far-Red Fluorescent Protein mKate Reveals pH-induced cis-trans Isomerization of the Chromophore. Authors: Pletnev, S. / Shcherbo, D. / Chudakov, D.M. / Pletneva, N. / Merzlyak, E.M. / Wlodawer, A. / Dauter, Z. / Pletnev, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 87.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 470.1 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27640.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CIT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 17.5% w/v PEG 3350, 0.07M citric acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→30 Å / Num. obs: 50567 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.041 / Χ2: 0.943 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Resolution: 1.75→29.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.676 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.121 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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