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Open data
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Basic information
Entry | Database: PDB / ID: 6ac4 | ||||||
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Title | Rat Xanthine oxidoreductase, D428N variant | ||||||
![]() | Xanthine dehydrogenase/oxidase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() response to azide / Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / negative regulation of vasculogenesis / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process ...response to azide / Butyrophilin (BTN) family interactions / hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / Azathioprine ADME / negative regulation of vasculogenesis / Purine catabolism / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / GMP catabolic process / xanthine dehydrogenase activity / amide catabolic process / response to carbon monoxide / adenosine catabolic process / deoxyinosine catabolic process / inosine catabolic process / regulation of epithelial cell differentiation / deoxyadenosine catabolic process / dAMP catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / AMP catabolic process / response to aluminum ion / IMP catabolic process / allantoin metabolic process / molybdopterin cofactor binding / nitrite reductase (NO-forming) activity / positive regulation of p38MAPK cascade / iron-sulfur cluster assembly / negative regulation of endothelial cell proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interleukin-1 / lactation / FAD binding / negative regulation of protein phosphorylation / sarcoplasmic reticulum / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / positive regulation of reactive oxygen species metabolic process / peroxisome / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / response to lipopolysaccharide / oxidoreductase activity / iron ion binding / negative regulation of gene expression / protein homodimerization activity / extracellular space / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okamoto, K. / Kawaguchi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Rat Xanthine oxidoreductase, D428A variant, NAD bound form Authors: Okamoto, K. / Kawaguchi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 550.6 KB | Display | ![]() |
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PDB format | ![]() | 437.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6a7xC ![]() 6ac1C ![]() 6ad4C ![]() 6adjC ![]() 6ajuC ![]() 1wygS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 146413.375 Da / Num. of mol.: 2 / Mutation: D428N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase #2: Chemical | #3: Chemical | ChemComp-FES / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 9-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20), VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→39.63 Å / Num. obs: 162134 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.19→2.247 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 26792 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WYG Resolution: 2.19→39.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.717 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 mean: 33.509 Å2
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Refinement step | Cycle: 1 / Resolution: 2.19→39.63 Å
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