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Yorodumi- PDB-8u41: OvsA from Halomonas utahensis, an ovoselenol-biosynthetic selenox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u41 | |||||||||
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Title | OvsA from Halomonas utahensis, an ovoselenol-biosynthetic selenoxide synthase in complex with histidine | |||||||||
Components | Selenoxide synthase OvsA | |||||||||
Keywords | OXIDOREDUCTASE / ovoselenol / selenium / selenoxide / nonheme iron | |||||||||
Function / homology | : / FORMIC ACID / HISTIDINE Function and homology information | |||||||||
Biological species | Halomonas utahensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 | 8u41.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u41.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 8u41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u41_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8u41_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8u41_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 8u41_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/8u41 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u41 | HTTPS FTP |
-Related structure data
Related structure data | 8u42C 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, 93 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 4.26 Å3/Da / Density % sol: 71.2 % / 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, 3.9 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: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 18, 2023 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→69.34 Å / Num. obs: 47873 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 74.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02925 / Rpim(I) all: 0.02925 / Rrim(I) all: 0.04136 / Net I/σ(I): 16.89 |
Reflection shell | Resolution: 2.72→2.817 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5307 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4740 / CC1/2: 0.654 / CC star: 0.889 / Rpim(I) all: 0.5307 / Rrim(I) all: 0.7505 / % possible all: 99.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→69.34 Å / SU ML: 0.468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0053 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: 78.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→69.34 Å
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Refine LS restraints |
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LS refinement shell |
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