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- PDB-7o3k: Structure of a monomeric variant (L135E) of Sandercyanin fluoresc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o3k | ||||||
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Title | Structure of a monomeric variant (L135E) of Sandercyanin fluorescent protein 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.7 KB | Display | ![]() |
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PDB format | ![]() | 31.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812.2 KB | Display | ![]() |
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Full document | ![]() | 816.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o2yC ![]() 7yx1C ![]() 5ez2S ![]() 7o32 C: citing same article ( S: Starting model for refinement |
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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: 20175.705 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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 26mg/mL 10% (w/v) PEG 1000, 10% (w/v) PEG 8000 |
-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: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→39.81 Å / Num. obs: 4795 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.07 / Rrim(I) all: 0.13 / Net I/av σ(I): 9 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 703 / CC1/2: 0.804 / Rpim(I) all: 0.35 / Rrim(I) all: 0.657 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EZ2 Resolution: 2.75→39.81 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 86.99 Å2 / Biso mean: 40.5199 Å2 / Biso min: 27.19 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→39.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %
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