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Open data
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Basic information
Entry | Database: PDB / ID: 7t8p | ||||||
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Title | CRYSTAL STRUCTURE OF T151V CAO1 | ||||||
![]() | Carotenoid oxygenase 1 | ||||||
![]() | OXIDOREDUCTASE / non-heme iron / beta propeller / stilbene / dioxygenase | ||||||
Function / homology | carotenoid dioxygenase activity / 9-cis-epoxycarotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / Carotenoid cleavage oxygenase 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Daruwalla, A. / Kiser, P.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CRYSTAL STRUCTURE OF T151V CAO1 Authors: Daruwalla, A. / Kiser, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 436.9 KB | Display | ![]() |
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PDB format | ![]() | 351.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 81.9 KB | Display | |
Data in CIF | ![]() | 121.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u8xS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 59495.965 Da / Num. of mol.: 4 / Mutation: T151V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: cao-1, NCU07008 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05 M HEPES pH 7 36% sodium polyacrylate 2100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 210666 / % possible obs: 99 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.542 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 32972 / CC1/2: 0.343 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U8X Resolution: 1.9→48.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.465 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.67 Å2 / Biso mean: 38.782 Å2 / Biso min: 23.34 Å2
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Refinement step | Cycle: final / Resolution: 1.9→48.08 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.901→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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