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Yorodumi- PDB-5ko7: Crystal structure of haliscomenobacter hydrossis iodotyrosine dei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ko7 | ||||||
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Title | Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN | ||||||
Components | Nitroreductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information iodotyrosine deiodinase / iodotyrosine deiodinase activity / FMN binding Similarity search - Function | ||||||
Biological species | Haliscomenobacter hydrossis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | ||||||
Authors | Ingavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S. | ||||||
Citation | Journal: Biochemistry / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ko7.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ko7.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ko7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/5ko7 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5ko7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ko8C 5krdC 3gb5S C: citing same article (ref.) 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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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.) Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O) (bacteria) Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2296 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: F4KU78 #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 80 mM Tris-HCl pH 8.5, 100 mM MgCl2, 24% (w/v) PEG 4000 and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→36.96 Å / Num. obs: 21635 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GB5 Resolution: 2.248→35.443 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.03 / 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: 2.248→35.443 Å
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Refine LS restraints |
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LS refinement shell |
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