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- PDB-5tuw: Crystal structure of Orange Carotenoid Protein with partial loss ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tuw | ||||||
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Title | Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore | ||||||
![]() | Orange carotenoid-binding protein | ||||||
![]() | Carotenoid binding protein / Photoreceptor / Photoprotection / Dynamic crystallography | ||||||
Function / homology | ![]() light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, X. / Bandara, S. / Ren, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Photoactivation mechanism of a carotenoid-based photoreceptor. Authors: Bandara, S. / Ren, Z. / Lu, L. / Zeng, X. / Shin, H. / Zhao, K.H. / Yang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 729.6 KB | Display | ![]() |
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PDB format | ![]() | 611.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tuxC ![]() 5tv0C ![]() 3mg1S C: citing same article ( S: Starting model for refinement |
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Similar 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: 35513.477 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EQ3 / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 mM sodium acetate (pH 4.5) 16% PEG 8000 2% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 85419 / % possible obs: 96 % / Redundancy: 1.9 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 1.9 % / Num. measured obs: 3806 / Rpim(I) all: 0.102 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MG1 Resolution: 2.302→41.49 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.302→41.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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