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Yorodumi- PDB-4yty: Structure of rat xanthine oxidoreductase, C535A/C992R/C1324S, NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yty | ||||||
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Title | Structure of rat xanthine oxidoreductase, C535A/C992R/C1324S, NADH bound form | ||||||
Components | Xanthine dehydrogenase/oxidase | ||||||
Keywords | OXIDOREDUCTASE / xanthine oxidoreductase / xanthine oxidase / xanthine dehydrogenase / D/O conversion | ||||||
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: 2.2 Å | ||||||
Authors | Nishino, T. / Okamoto, K. / Kawaguchi, Y. / Matsumura, T. / Eger, B.T. / Pai, E.F. | ||||||
Citation | Journal: Febs J. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yty.cif.gz | 549.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yty.ent.gz | 435 KB | Display | PDB format |
PDBx/mmJSON format | 4yty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4yty ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4yty | HTTPS FTP |
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-Related structure data
Related structure data | 4yrwC 4yswC 4ytzC 3an1S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 146420.281 Da / Num. of mol.: 2 / Mutation: C535A, C992R, C1324S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Xdh / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 8 types, 1424 molecules
#2: Chemical | ChemComp-FES / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-URC / | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: 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: 2.64 Å3/Da / Density % sol: 53.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, lithium formate, DTT, sodium salicylate, EDTA, glycerol, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.5 Å / Num. obs: 153088 / % possible obs: 99.7 % / Redundancy: 7.4 % / Net I/σ(I): 18.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AN1 Resolution: 2.2→49.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.579 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.192 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 192.89 Å2 / Biso mean: 21.237 Å2 / Biso min: 5.54 Å2
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Refinement step | Cycle: final / Resolution: 2.2→49.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.26 Å / Total num. of bins used: 20
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