+Open data
-Basic information
Entry | Database: PDB / ID: 3eub | ||||||
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Title | Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine | ||||||
Components | (Xanthine dehydrogenase/oxidase) x 3 | ||||||
Keywords | OXIDOREDUCTASE / enzyme catalysis / desulfo / substrate orientation / xanthine / FAD / Flavoprotein / Iron / Iron-sulfur / Metal-binding / Molybdenum / NAD / Peroxisome | ||||||
Function / homology | Function and homology information xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding ...xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Pauff, J.M. / Cao, H. / Hille, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: CRYSTAL STRUCTURES IN COMPLEX WITH XANTHINE AND LUMAZINE. Authors: Pauff, J.M. / Cao, H. / Hille, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eub.cif.gz | 941.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eub.ent.gz | 752.8 KB | Display | PDB format |
PDBx/mmJSON format | 3eub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3eub ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eub | HTTPS FTP |
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-Related structure data
Related structure data | 3etrC 1fiqS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Dom-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
-Protein , 3 types, 12 molecules AJS2BKT3CLU4
#1: Protein | Mass: 18134.078 Da / Num. of mol.: 4 / Fragment: 2Fe-2S ferredoxin-type domain, residues 1-165 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: Bovine Milk References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase #2: Protein | Mass: 34024.590 Da / Num. of mol.: 4 / Fragment: AD-binding PCMH-type domain, residues 224-528 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: Bovine Milk References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase #3: Protein | Mass: 83835.273 Da / Num. of mol.: 4 / Fragment: residues 571-1332 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: Bovine Milk References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 5 types, 24 molecules
#4: Chemical | ChemComp-FES / #5: Chemical | ChemComp-FAD / #6: Chemical | ChemComp-MTE / #7: Chemical | ChemComp-MOM / #8: Chemical | ChemComp-XAN / |
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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: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7.2 / Details: PEG 8000, pH 7.2, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→141.42 Å / Num. obs: 119504 |
Reflection shell | Resolution: 2.6→2.668 Å / Num. unique all: 5403 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FIQ Resolution: 2.6→33.08 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.826 / WRfactor Rfree: 0.308 / WRfactor Rwork: 0.246 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.823 / SU B: 12.029 / SU ML: 0.263 / SU Rfree: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, MOM IS IN THE DESULFO FORM WITH AN ADDITIONAL OXYGEN IN PLACE OF THE SULFUR IN THE COORDINATION SPHERE
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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 max: 50.14 Å2 / Biso mean: 13.895 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→33.08 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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