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Yorodumi- PDB-8k5i: The structure of SenA in complex with N,N,N-trimethyl-histidine a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k5i | ||||||
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Title | The structure of SenA in complex with N,N,N-trimethyl-histidine and thioglucose | ||||||
Components | selenoneine synthase SenA | ||||||
Keywords | METAL BINDING PROTEIN / selenoneine synthase / nonheme iron enzyme | ||||||
Function / homology | N,N,N-trimethyl-histidine / : / 1-thio-beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Variovorax paradoxus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Liu, M. / Yang, Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k5i.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k5i.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 8k5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/8k5i ftp://data.pdbj.org/pub/pdb/validation_reports/k5/8k5i | HTTPS FTP |
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-Related structure data
Related structure data | 8k5jC 8k5kC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 47102.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Variovorax paradoxus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#4: Sugar | ChemComp-GS1 / |
-Non-polymers , 5 types, 447 molecules
#2: Chemical | ChemComp-FE / | ||||
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#3: Chemical | ChemComp-AVJ / | ||||
#5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-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: 2.16 Å3/Da / Density % sol: 43.07 % |
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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: May 12, 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: 1.92→33.2 Å / Num. obs: 31836 / % possible obs: 99.7 % / Redundancy: 5.07 % / Rmerge(I) obs: 0.0792 / Net I/σ(I): 12.65 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.2694 / Mean I/σ(I) obs: 3.31 / Num. unique obs: 1370 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→33.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.72 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.864 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→33.2 Å
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