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- PDB-7o2y: Sandercyanin Fluorescent Protein variant V71E bound to biliverdin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o2y | ||||||
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Title | Sandercyanin Fluorescent Protein variant V71E bound to biliverdin IX-alpha | ||||||
![]() | Sandercyanin Fluorescent Protein | ||||||
![]() | FLUORESCENT PROTEIN / Blue fish protein / lipocalin / Biliverdin-binding protein / red-fluorescent protein | ||||||
Function / homology | ![]() pigment binding / response to reactive oxygen species / lipid metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghosh, S. / Yadav, K. / Ramaswamy, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Modulation of biliverdin dynamics and spectral properties by Sandercyanin. Authors: Ghosh, S. / Mondal, S. / Yadav, K. / Aggarwal, S. / Schaefer, W.F. / Narayana, C. / Subramanian, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 832.8 KB | Display | ![]() |
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Full document | ![]() | 834.2 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o3kC ![]() 7yx1C ![]() 5ez2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 20189.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-BLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11mg/mL 0.2M calcium chloride dihydrate, 20% (w/v) PEG 3350, pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.84 Å / Num. obs: 41927 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 3399 / CC1/2: 0.306 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EZ2 Resolution: 2.5→36.56 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.641 / SU ML: 0.202 / Cross valid method: FREE R-VALUE / ESU R: 1.4 / ESU R Free: 0.319 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→36.56 Å
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Refine LS restraints |
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LS refinement shell |
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