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Yorodumi- PDB-2e1q: Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1q | ||||||
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Title | Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val | ||||||
Components | Xanthine dehydrogenase/oxidase | ||||||
Keywords | OXIDOREDUCTASE / xanthine oxidase / molybdenum cofactor / FAD | ||||||
Function / homology | Function and homology information hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase ...hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / 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 / Butyrophilin (BTN) family interactions / amide catabolic process / adenosine catabolic process / deoxyinosine catabolic process / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / AMP catabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / molybdopterin cofactor binding / Azathioprine ADME / 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 / lactation / FAD binding / negative regulation of protein phosphorylation / sarcoplasmic reticulum / 2 iron, 2 sulfur cluster binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of reactive oxygen species metabolic process / peroxisome / flavin adenine dinucleotide binding / iron ion binding / negative regulation of gene expression / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yamaguchi, Y. / Matsumura, T. / Ichida, K. / Okamoto, K. / Nishino, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2007 Title: Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and ...Title: Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate Authors: Yamaguchi, Y. / Matsumura, T. / Ichida, K. / Okamoto, K. / Nishino, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1q.cif.gz | 1022.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1q.ent.gz | 831.3 KB | Display | PDB format |
PDBx/mmJSON format | 2e1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1q ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1q | HTTPS FTP |
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-Related structure data
Related structure data | 1fo4S 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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2 |
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Unit cell |
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Details | The biological assembly is a homodimer. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 146571.797 Da / Num. of mol.: 4 / Mutation: E803V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 References: UniProt: P47989, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 8 types, 985 molecules
#2: Chemical | ChemComp-BCT / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-FES / #5: Chemical | ChemComp-FAD / #6: Chemical | ChemComp-MTE / #7: Chemical | ChemComp-MOM / #8: Chemical | ChemComp-SAL / #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: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 5% PEG 8000, 0.05M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 202081 / Num. obs: 192029 / % possible obs: 95 % / Rsym value: 0.085 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FO4 Resolution: 2.6→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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