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Yorodumi- PDB-8ux5: OvsA M401Y/Q430N/A431F from Halomonas utahensis, a hercynine-bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ux5 | |||||||||
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Title | OvsA M401Y/Q430N/A431F from Halomonas utahensis, a hercynine-binding variant with selenoneine-biosynthetic activity | |||||||||
Components | Selenoxide synthase OvsA | |||||||||
Keywords | OXIDOREDUCTASE / hercynine / selenoneine / selenium / selenoxide | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Halomonas utahensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å | |||||||||
Authors | Ireland, K.A. / Davis, K.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Chem. / Year: 2024 Title: Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution. Authors: Kayrouz, C.M. / Ireland, K.A. / Ying, V.Y. / Davis, K.M. / Seyedsayamdost, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ux5.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ux5.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ux5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ux5_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 8ux5_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 8ux5_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 8ux5_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/8ux5 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/8ux5 | HTTPS FTP |
-Related structure data
Related structure data | 8u41C 8u42C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54987.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomonas utahensis (bacteria) / Strain: DSM 3051 / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.45 Å3/Da / Density % sol: 72.4 % / Description: Clear hexagonal rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6, 3.5 M sodium formate, 10 mM sarcosine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 11, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→29.09 Å / Num. obs: 35167 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 106.98 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03673 / Rpim(I) all: 0.03673 / Rrim(I) all: 0.05194 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.06→3.169 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6614 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 3456 / CC1/2: 0.501 / CC star: 0.817 / Rpim(I) all: 0.6614 / Rrim(I) all: 0.9353 / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→29.09 Å / SU ML: 0.4654 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4876 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→29.09 Å
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Refine LS restraints |
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LS refinement shell |
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