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- PDB-4ytz: Rat xanthine oxidoreductase, C-terminal deletion protein variant,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ytz | ||||||
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Title | Rat xanthine oxidoreductase, C-terminal deletion protein variant, crystal grown without dithiothreitol | ||||||
![]() | Xanthine dehydrogenase/oxidase | ||||||
![]() | OXIDOREDUCTASE / xanthine oxidoreductase / xanthine oxidase / xanthine dehydrogenase / D/O conversion | ||||||
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 / deoxyinosine catabolic process / adenosine catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / inosine catabolic process / regulation of epithelial cell differentiation / deoxyadenosine catabolic process / dAMP catabolic process / response to aluminum ion / AMP catabolic process / 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 / peroxisome / positive regulation of reactive oxygen species metabolic process / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Nishino, T. / Okamoto, K. / Kawaguchi, Y. / Matsumura, T. / Eger, B.T. / Pai, E.F. / Nishino, T. | ||||||
![]() | ![]() Title: The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase Authors: Nishino, T. / Okamoto, K. / Kawaguchi, Y. / Matsumura, T. / Eger, B.T. / Pai, E.F. / Nishino, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 504 KB | Display | ![]() |
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PDB format | ![]() | 404.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 86.1 KB | Display | |
Data in CIF | ![]() | 119 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yrwC ![]() 4yswC ![]() 4ytyC ![]() 3an1S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 144652.344 Da / Num. of mol.: 2 / Fragment: UNP residues 1-1315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 6 types, 119 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/URC.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/URC.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEGl 8000, lithium formate, sodium salicylate, EDTA, glycerol, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 13, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 135086 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Χ2: 1.011 / Net I/av σ(I): 15.242 / Net I/σ(I): 14.7 / Num. measured all: 468751 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AN1 Resolution: 2.3→29.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.389 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.46 Å2 / Biso mean: 35.084 Å2 / Biso min: 11.38 Å2
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Refinement step | Cycle: final / Resolution: 2.3→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.297→2.356 Å / Total num. of bins used: 20
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