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Yorodumi- PDB-8u42: OvsA from Halomonas utahensis, a selenoxide synthase involved in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u42 | |||||||||
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Title | OvsA from Halomonas utahensis, a selenoxide synthase involved in ovoselenol biosynthesis | |||||||||
Components | Selenoxide synthase OvsA | |||||||||
Keywords | OXIDOREDUCTASE / ovoselenol / selenium / selenoxide / nonheme iron | |||||||||
Function / homology | : / FORMIC ACID Function and homology information | |||||||||
Biological species | Halomonas utahensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 8u42.cif.gz | 227.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u42.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 8u42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u42_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 8u42_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 8u42_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 8u42_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/8u42 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u42 | HTTPS FTP |
-Related structure data
Related structure data | 8u41C 8ux5C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54745.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomonas utahensis (bacteria) / Strain: DSM 3051 / Gene: CK501_04640 / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 5 types, 723 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 3.58 Å3/Da / Density % sol: 65.6 % / Description: Clear hexagonal rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1 M sodium acetate pH 4.8, 3.5 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2023 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→57.71 Å / Num. obs: 98747 / % possible obs: 95.18 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.07203 / Rpim(I) all: 0.07203 / Rrim(I) all: 0.1019 / Net I/σ(I): 6.57 |
Reflection shell | Resolution: 2→2.071 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6019 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 9984 / CC1/2: 0.562 / CC star: 0.848 / Rpim(I) all: 0.6019 / Rrim(I) all: 0.8512 / % possible all: 96.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→57.71 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.575 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: 35.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→57.71 Å
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Refine LS restraints |
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LS refinement shell |
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