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Open data
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Basic information
Entry | Database: PDB / ID: 8k5k | ||||||
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Title | The structure of SenA | ||||||
![]() | selenoneine synthase SenA | ||||||
![]() | METAL BINDING PROTEIN / selenoneine synthase / nonheme iron enzyme | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, M. / Yang, Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into a novel nonheme iron-dependent oxygenase in selenoneine biosynthesis. Authors: Liu, M. / Yang, Y. / Huang, J.W. / Dai, L. / Zheng, Y. / Cheng, S. / He, H. / Chen, C.C. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 921.5 KB | Display | ![]() |
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Full document | ![]() | 925 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k5iC ![]() 8k5jC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47102.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-FE / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 6000, 0.1 M Tris/HCl pH 8.0, 0.2 M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Apr 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→34.38 Å / Num. obs: 37959 / % possible obs: 99.4 % / Redundancy: 7.08 % / Rmerge(I) obs: 0.0696 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 4.47 % / Rmerge(I) obs: 0.4439 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 1745 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.134 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→34.38 Å
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Refine LS restraints |
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