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Yorodumi- PDB-3gb5: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gb5 | ||||||
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Title | Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN | ||||||
Components | Iodotyrosine dehalogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / IYD / iodide salvage / flavoprotein / FMN / Membrane / NADP / Transmembrane | ||||||
Function / homology | Function and homology information Thyroxine biosynthesis / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / thyroid hormone metabolic process / cytoplasmic vesicle membrane / FMN binding / oxidoreductase activity / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Thomas, S.R. / McTamney, P.M. / Adler, J.M. / LaRonde-LeBlanc, N. / Rokita, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands. Authors: Thomas, S.R. / McTamney, P.M. / Adler, J.M. / Laronde-Leblanc, N. / 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 | 3gb5.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gb5.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gb5_validation.pdf.gz | 827.2 KB | Display | wwPDB validaton report |
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Full document | 3gb5_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 3gb5_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3gb5_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gb5 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gb5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT IS CONFIRMED BY ULTRACENTRIFUGATION |
-Components
#1: Protein | Mass: 29987.398 Da / Num. of mol.: 1 / Fragment: UNP residues 34-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Iyd, Dehal1 / Plasmid: pFASTBAC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9DCX8 | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 3000, 0.1 M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.653 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2008 |
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.653 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 36382 / Num. obs: 36382 / % possible obs: 99.8 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.764 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. The Friedel pairs were used in phasing. 2. 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 max: 76.58 Å2 / Biso mean: 32.568 Å2 / Biso min: 19.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.5688 Å / Origin y: 45.6643 Å / Origin z: 26.0996 Å
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