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Open data
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Basic information
Entry | Database: PDB / ID: 6j95 | ||||||
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Title | Crystal structure of CYP97A3 in complex with retinal | ||||||
![]() | Protein LUTEIN DEFICIENT 5, chloroplastic | ||||||
![]() | OXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450 | ||||||
Function / homology | ![]() carotene beta-ring hydroxylase activity / xanthophyll biosynthetic process / carotenoid biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast envelope / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niu, G. / Guo, Q. / Wang, J. / Zhao, S. | ||||||
![]() | ![]() Title: Structural basis for plant lutein biosynthesis from alpha-carotene. Authors: Niu, G. / Guo, Q. / Wang, J. / Zhao, S. / He, Y. / Liu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.9 KB | Display | ![]() |
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PDB format | ![]() | 168.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 815.9 KB | Display | ![]() |
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Full document | ![]() | 818.7 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j94C ![]() 6l8hC ![]() 6l8iC ![]() 6l8jC ![]() 4kf2S S: Starting model for refinement C: citing same article ( |
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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: 58463.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q93VK5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-RET / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 289 K / Method: liquid diffusion / Details: 0.2 M potassium sulfate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 36341 / % possible obs: 99.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3557 / CC1/2: 0.875 / Rpim(I) all: 0.223 / Rrim(I) all: 0.734 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KF2 Resolution: 2.002→47.632 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.16 Å2 / Biso mean: 34.3516 Å2 / Biso min: 15.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.002→47.632 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: -22.1556 Å / Origin y: 3.9029 Å / Origin z: -13.944 Å
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Refinement TLS group | Selection details: all |