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- PDB-3pjb: Crystal structure of red fluorescent protein eqFP578 crystallized... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pjb | ||||||
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Title | Crystal structure of red fluorescent protein eqFP578 crystallized at pH 4.0 | ||||||
![]() | Red fluorescent protein eqFP578 | ||||||
![]() | FLUORESCENT PROTEIN / eqFP578 / red fluorescent protein / beta-barrel / Biomarker / Met-Tyr-Gly chromophore | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP578![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pletnev, S. / Pletneva, N.V. / Pletnev, V.Z. | ||||||
![]() | ![]() Title: Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore. Authors: Pletneva, N.V. / Pletnev, V.Z. / Shemiakina, I.I. / Chudakov, D.M. / Artemyev, I. / Wlodawer, A. / Dauter, Z. / Pletnev, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.6 KB | Display | ![]() |
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PDB format | ![]() | 155.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.9 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 33.6 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
#1: Protein | Mass: 26093.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.4 M ammonium sulfate, pH 4.0, 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 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→50 Å / Num. obs: 76637 / % possible obs: 97.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.062 / Χ2: 0.997 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.065 Å2 / ksol: 0.455 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.55 Å2 / Biso mean: 27.6203 Å2 / Biso min: 10.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→34.749 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: 10
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