+Open data
-Basic information
Entry | Database: PDB / ID: 6j94 | ||||||
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Title | Crystal structure of CYP97A3 | ||||||
Components | Protein LUTEIN DEFICIENT 5, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / lutein biosynthesis / photosynthesis / monooxygenase / carotenoid / P450 | ||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Niu, G. / Guo, Q. / Wang, J. / Zhao, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j94.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j94.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j94_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6j94_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6j94_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 6j94_validation.cif.gz | 59.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/6j94 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j94 | HTTPS FTP |
-Related structure data
Related structure data | 6j95C 6l8hC 6l8iC 6l8jC 4kf2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58463.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP97A3, LUT5, At1g31800, F5M6.19 / Production host: Escherichia coli (E. coli) References: UniProt: Q93VK5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 289 K / Method: liquid diffusion / pH: 6.5 / Details: 0.1 M MES, 12% (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 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: 2.4→50 Å / Num. obs: 48368 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.23 Å2 / CC1/2: 0.937 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / Num. unique obs: 4769 / CC1/2: 0.752 / Rpim(I) all: 0.409 / Rrim(I) all: 0.807 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KF2 Resolution: 2.401→41.963 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.94 Å2 / Biso mean: 20.87 Å2 / Biso min: 2.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.401→41.963 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: 17
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