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Yorodumi- PDB-4ttc: Crystal structure of homo sapiens IODOTYROSINE DEIODINASE bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ttc | ||||||
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Title | Crystal structure of homo sapiens IODOTYROSINE DEIODINASE bound to FMN and mono-iodotyrosine (MIT) | ||||||
Components | Iodotyrosine dehalogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / MEMBRANE / TRANSMEMBRANE / DEHALOGENASE / IODIDE SALVAGE / MONO-IODOTYROSINE / MIT | ||||||
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: 2.65 Å | ||||||
Authors | Chuenchor, W. / Hu, J. / Rokita, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: A Switch between One- and Two-electron Chemistry of the Human Flavoprotein Iodotyrosine Deiodinase Is Controlled by Substrate. Authors: Hu, J. / Chuenchor, W. / 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 | 4ttc.cif.gz | 559.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ttc.ent.gz | 461.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ttc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ttc_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 4ttc_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 4ttc_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 4ttc_validation.cif.gz | 67.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4ttc ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4ttc | HTTPS FTP |
-Related 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: 30655.057 Da / Num. of mol.: 6 / Fragment: UNP residues 32-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IYD, C6orf71, DEHAL1 / Plasmid: pET28-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: Q6PHW0, EC: 1.22.1.1 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-IYR / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % / Description: Needle-Shaped Crystal |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.15 M sodium acetate, 85 mM Tris-HCl, 25.5 % w/v polyethylene glycol 4,000 and 15 % glycerol PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Single wavelength |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 54565 / Num. obs: 54565 / % possible obs: 100 % / Redundancy: 9.6 % / Rsym value: 0.088 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1000202202 Resolution: 2.65→44.858 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→44.858 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.0538 Å / Origin y: 109.0423 Å / Origin z: 16.9982 Å
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Refinement TLS group | Selection details: all |