+Open data
-Basic information
Entry | Database: PDB / ID: 6a16 | ||||||
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Title | Crystal structure of CYP90B1 in complex with uniconazole | ||||||
Components | Cytochrome P450 90B1 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / phytohormone / brassinosteroid / uniconazole | ||||||
Function / homology | Function and homology information steroid 22S-hydroxylase / steroid 22-alpha hydroxylase activity / brassinosteroid biosynthetic process / fatty acid alpha-hydroxylase activity / leaf shaping / response to brassinosteroid / unidimensional cell growth / jasmonic acid mediated signaling pathway / leaf development / response to jasmonic acid ...steroid 22S-hydroxylase / steroid 22-alpha hydroxylase activity / brassinosteroid biosynthetic process / fatty acid alpha-hydroxylase activity / leaf shaping / response to brassinosteroid / unidimensional cell growth / jasmonic acid mediated signaling pathway / leaf development / response to jasmonic acid / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding / heme binding / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.998 Å | ||||||
Authors | Fujiyama, K. / Hino, T. / Kanadani, M. / Mizutani, M. / Nagano, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat.Plants / Year: 2019 Title: Structural insights into a key step of brassinosteroid biosynthesis and its inhibition. Authors: Fujiyama, K. / Hino, T. / Kanadani, M. / Watanabe, B. / Jae Lee, H. / Mizutani, M. / Nagano, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a16.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a16.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/6a16 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/6a16 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56490.469 Da / Num. of mol.: 1 / Mutation: M1-L28 was substituted with MA, P506L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP90B1, DWF4, At3g50660, T3A5.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: O64989, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 348 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-UCZ / ( | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.20 M potassium chloride, 0.40 M sodium chloride, 22%(w/v) PEG3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.998→45.57 Å / Num. obs: 35966 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.1534 / Rrim(I) all: 0.1792 / Net I/σ(I): 9.16 |
Reflection shell | Resolution: 1.998→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7386 / Num. unique obs: 3473 / CC1/2: 0.639 / Rrim(I) all: 0.8625 / % possible all: 97.61 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.998→45.567 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.998→45.567 Å
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Refine LS restraints |
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LS refinement shell |
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