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Yorodumi- PDB-6kun: Crystal structure of dioxygenase for auxin oxidation (DAO) in rice -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kun | |||||||||
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Title | Crystal structure of dioxygenase for auxin oxidation (DAO) in rice | |||||||||
Components | 2-oxoglutarate-dependent dioxygenase DAO | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Jelly Rolls / Metal Ion Binding / Oxygenase | |||||||||
Function / homology | Function and homology information auxin catabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Oryza sativa subsp. indica (long-grained rice) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | |||||||||
Authors | Takehara, S. / Mikami, B. / Sakuraba, S. / Matsuoka, M. / Ueguchi-Tanaka, M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin. Authors: Takehara, S. / Sakuraba, S. / Mikami, B. / Yoshida, H. / Yoshimura, H. / Itoh, A. / Endo, M. / Watanabe, N. / Nagae, T. / Matsuoka, M. / Ueguchi-Tanaka, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kun.cif.gz | 247.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kun.ent.gz | 198.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kun_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6kun_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6kun_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 6kun_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kun ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kun | HTTPS FTP |
-Related structure data
Related structure data | 6ku3SC 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: 32141.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice) Gene: DAO, OsI_16300, OSIGBa0106G07.8 / Production host: Escherichia coli (E. coli) References: UniProt: Q01IX6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium acetate, 0.2 M ammonium sulfate and 22% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 38070 / % possible obs: 100 % / Redundancy: 9.5 % / Rsym value: 0.054 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 2675 / Rsym value: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KU3 Resolution: 2.002→40.3073 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.58 Å2 / Biso mean: 35.8703 Å2 / Biso min: 9.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.002→40.3073 Å
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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: 37.5395 Å / Origin y: -9.0634 Å / Origin z: -24.0334 Å
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Refinement TLS group |
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