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Yorodumi- PDB-6pz0: Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pz0 | ||||||
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Title | Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and L-Tyrosine | ||||||
Components | iodotyrosine deiodinase | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / dehalogenase / thermophile / halotyrosine | ||||||
Function / homology | Function and homology information L-tyrosine binding / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / FMN binding Similarity search - Function | ||||||
Biological species | Thermotoga neapolitana DSM 4359 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sun, Z. / Kavran, J.M. / Rokita, S.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana. Authors: Sun, Z. / Xu, B. / Spisak, S. / Kavran, 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 | 6pz0.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pz0.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 6pz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/6pz0 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/6pz0 | HTTPS FTP |
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-Related structure data
Related structure data | 6q1lC 5k08S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22892.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga neapolitana DSM 4359 (bacteria) Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: CTN_0569 / Production host: Escherichia coli (E. coli) / References: UniProt: B9K712, iodotyrosine deiodinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | 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: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate, pH 4.5, 3 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.799→35.67 Å / Num. obs: 34678 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5K08 Resolution: 1.8→35.669 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 18.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.14 Å2 / Biso mean: 23.8478 Å2 / Biso min: 6.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→35.669 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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