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- PDB-3una: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NAD Bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 3una | ||||||
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Title | Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NAD Bound | ||||||
![]() | Xanthine dehydrogenase/oxidase | ||||||
![]() | OXIDOREDUCTASE / Xanthine Dehydrogenase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eger, B.T. / Okamoto, K. / Nishino, T. / Pai, E.F. | ||||||
![]() | ![]() Title: Protein conformational gating of enzymatic activity in xanthine oxidoreductase. Authors: Ishikita, H. / Eger, B.T. / Okamoto, K. / Nishino, T. / Pai, E.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 551.3 KB | Display | ![]() |
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PDB format | ![]() | 439.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 105.3 KB | Display | |
Data in CIF | ![]() | 152.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ax7C ![]() 3ax9C ![]() 3uncC ![]() 3uniC ![]() 1fo4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 146970.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Isolated from Milk / Source: (natural) ![]() ![]() References: UniProt: P80457, xanthine dehydrogenase, xanthine oxidase |
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-Non-polymers , 10 types, 1533 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-GOL / #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 293 K / Method: sitting drop batch slide / pH: 7.5 Details: 12 mg/ml Xanthine Dehydrogenase (from Bovine Milk), 8 % Polyethylene Glycol 4000, 30 % Glycerol, 5 mM Dithiothreitol, 0.5 mM Sodium Salicylate, 0.2 m Ethylenediaminetetraacetic Acid, 16.65 ...Details: 12 mg/ml Xanthine Dehydrogenase (from Bovine Milk), 8 % Polyethylene Glycol 4000, 30 % Glycerol, 5 mM Dithiothreitol, 0.5 mM Sodium Salicylate, 0.2 m Ethylenediaminetetraacetic Acid, 16.65 mM Sodium Pyrophosphate (pH 8.5), 25 mM Potasium Phosphate (pH 6.5). , Sitting Drop Batch Slide, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99077 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 233141 / Num. obs: 232449 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / Num. unique all: 11481 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1FO4 Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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