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- PDB-6sgm: Crystal structure of monooxygenase RutA complexed with 4-Thiouracil. -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sgm | |||||||||
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Title | Crystal structure of monooxygenase RutA complexed with 4-Thiouracil. | |||||||||
![]() | Pyrimidine monooxygenase RutA | |||||||||
![]() | FLAVOPROTEIN / monooxygenase / RutA / FMN / flavin-N5-oxide / bioengineering | |||||||||
Function / homology | ![]() pyrimidine oxygenase / uracil oxygenase activity / alkanesulfonate monooxygenase activity / thymine catabolic process / alkanesulfonate catabolic process / pyrimidine nucleobase catabolic process / uracil catabolic process / nitrogen utilization / monooxygenase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saleem-Batcha, R. / Matthews, A. / Teufel, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Authors: Matthews, A. / Saleem-Batcha, R. / Sanders, J.N. / Stull, F. / Houk, K.N. / Teufel, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6sggC ![]() 6sglC ![]() 6sgnC ![]() 6teeC ![]() 6tefC ![]() 6tegC ![]() 5wanS ![]() 6sgj C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 39980.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: rutA, ycdM, b1012, JW0997 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-LDB / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v),1 mM FMN, 1 mM 4-Thiouracil |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 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→48 Å / Num. obs: 29258 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.99 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2→2.11 Å / Num. unique obs: 4194 / CC1/2: 0.953 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WAN Resolution: 2→43.822 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.696 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.156 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.855 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.822 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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