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Yorodumi- PDB-2e3t: Crystal structure of rat xanthine oxidoreductase mutant (W335A an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e3t | ||||||
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Title | Crystal structure of rat xanthine oxidoreductase mutant (W335A and F336L) | ||||||
Components | Xanthine dehydrogenase/oxidase | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase to oxidase 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 / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Asai, R. / Nishino, T. / Matsumura, T. / Okamoto, K. / Pai, E.F. / Nishino, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2007 Title: Two mutations convert mammalian xanthine oxidoreductase to highly superoxide-productive xanthine oxidase Authors: Asai, R. / Nishino, T. / Matsumura, T. / Okamoto, K. / Igarashi, K. / 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 | 2e3t.cif.gz | 541.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e3t.ent.gz | 432.8 KB | Display | PDB format |
PDBx/mmJSON format | 2e3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/2e3t ftp://data.pdbj.org/pub/pdb/validation_reports/e3/2e3t | 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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Unit cell |
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Details | The biological assembly is a homodimer. Both chains are included in the coordinate file. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 146265.203 Da / Num. of mol.: 2 / Mutation: W335A, F336L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P22985, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 7 types, 1416 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-FES / #6: Chemical | #7: Chemical | #8: 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: 2.68 Å3/Da / Density % sol: 54.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.2 Details: 10% Polyethylene glycol 8000, 0.6M Lithium sulfate, 5mM dithiothreitol, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES, pH 6.20, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→25 Å / Num. obs: 143627 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 8.2 % / Rsym value: 0.08 |
Reflection shell | Resolution: 2.28→2.42 Å / Redundancy: 7.4 % / Num. unique all: 20624 / Rsym value: 0.387 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FO4 Resolution: 2.28→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.28→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.32 Å /
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