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Open data
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Basic information
Entry | Database: PDB / ID: 6l8i | ||||||
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Title | Crystal structure of CYP97A3 mutant S290D/W300L/S304V | ||||||
![]() | 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. / Liu, L. | ||||||
![]() | ![]() 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 | ![]() | 115.5 KB | Display | ![]() |
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PDB format | ![]() | 83.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.6 KB | Display | ![]() |
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Full document | ![]() | 820.4 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j94C ![]() 6j95C ![]() 6l8hC ![]() 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: 58430.836 Da / Num. of mol.: 1 / Mutation: S290D,W300L,S304V 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: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 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: 1.7→50 Å / Num. obs: 58443 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Net I/σ(I): 55.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 5770 / CC1/2: 0.97 / Rpim(I) all: 0.153 / Rrim(I) all: 0.543 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KF2 Resolution: 1.7→29.035 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.68 Å2 / Biso mean: 35.91 Å2 / Biso min: 19.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→29.035 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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