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Yorodumi- PDB-5yak: The crystal structure of human IYD Thr239 mutant with ligand 3-Fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yak | ||||||
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Title | The crystal structure of human IYD Thr239 mutant with ligand 3-Fluorotyrosine (F-Tyr) | ||||||
Components | Iodotyrosine deiodinase 1 | ||||||
Keywords | OXIDOREDUCTASE / hIYD / FMN / MFT / T239A mutant | ||||||
Function / homology | Function and homology information iodotyrosine deiodinase / iodotyrosine deiodinase activity / Thyroxine biosynthesis / tyrosine metabolic process / thyroid hormone metabolic process / cytoplasmic vesicle membrane / FMN binding / oxidoreductase activity / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hu, J.M. / Rokita, S.E. / Schlessman, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2019 Title: Redox control of iodotyrosine deiodinase Authors: Hu, J. / Su, Q. / Schlessman, J.L. / Rokita, S.E. #1: Journal: To Be Published Title: The role of Thr239 on the catalysis of hIYD Authors: Hu, J.M. / Rokita, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yak.cif.gz | 286 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yak.ent.gz | 229.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yak_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 5yak_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5yak_validation.xml.gz | 51 KB | Display | |
Data in CIF | 5yak_validation.cif.gz | 69.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/5yak ftp://data.pdbj.org/pub/pdb/validation_reports/ya/5yak | HTTPS FTP |
-Related structure data
Related structure data | 4ttcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30537.951 Da / Num. of mol.: 6 / Fragment: UNP residues 32-289 / Mutation: T239A Source method: isolated from a genetically manipulated source Details: FMN(flavin mononucleotide) YOF(3-monofluorotyrosine) Source: (gene. exp.) Homo sapiens (human) / Gene: IYD, C6orf71, DEHAL1 / Plasmid: pET28-SUMO / Details (production host): sumo fusion N-terminal / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q6PHW0, iodotyrosine deiodinase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-YOF / #4: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.17 M sodium acetate, 85 mM Tris-HCl (pH 8.5), 22.5 % w/v polyethylene glycol 4,000 and 15 % glycerol. PH range: 7.4-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.52 Å / Num. obs: 82734 / % possible obs: 100 % / Redundancy: 8 % / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.093 / Rsym value: 0.084 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TTC Resolution: 2.3→46.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.199 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.406 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→46.52 Å
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Refine LS restraints |
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