+Open data
-Basic information
Entry | Database: PDB / ID: 6aju | ||||||
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Title | Rat Xanthine oxidoreductase | ||||||
Components | Xanthine dehydrogenase/oxidase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 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 / IMP catabolic process / response to aluminum ion / 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 / flavin adenine dinucleotide binding / cellular response to tumor necrosis factor / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Okamoto, K. / Kawaguchi, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Rat Xanthine oxidoreductase, D428A variant, NAD bound form Authors: Okamoto, K. / Kawaguchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aju.cif.gz | 536.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aju.ent.gz | 428 KB | Display | PDB format |
PDBx/mmJSON format | 6aju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/6aju ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6aju | HTTPS FTP |
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-Related structure data
Related structure data | 6a7xC 6ac1C 6ac4C 6ad4C 6adjC 1wygS 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
-Protein , 1 types, 2 molecules AF
#1: Protein | Mass: 146414.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Xdh / Production host: Escherichia coli (E. coli) References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 5 types, 1300 molecules
#2: Chemical | ChemComp-FES / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 295 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) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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: 1.94→38.89 Å / Num. obs: 224074 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.095 / Χ2: 0.999 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.94→1.99 Å / Rmerge(I) obs: 0.249 / Num. unique obs: 22202 / % possible all: 99.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WYG Resolution: 1.94→38.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.059 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / 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: 23.577 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→38.89 Å
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