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- PDB-5krd: Crystal structure of haliscomenobacter hydrossis iodotyrosine dei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5krd | ||||||
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Title | Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and 2-iodophenol (2IP) | ||||||
![]() | Nitroreductase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / thyroid hormone metabolic process / FMN binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ingavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S. | ||||||
![]() | ![]() Title: Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase. Authors: Ingavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.7 KB | Display | ![]() |
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PDB format | ![]() | 209 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ko7C ![]() 5ko8C ![]() 3gb5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26165.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2296 Production host: ![]() ![]() References: UniProt: F4KU78 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM Tris-HCl pH 9, 200 mM MgCl2, 2 mM 2-iodophenol, 17% (w/v) PEG 8000, 17% glycerol and 10% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 36524 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GB5 Resolution: 2.103→19.994 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.41 / 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: 2.103→19.994 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: -50.0449 Å / Origin y: -31.2175 Å / Origin z: 7.5743 Å
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Refinement TLS group | Selection details: all |