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- PDB-1fo4: CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fo4 | ||||||
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Title | CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK | ||||||
![]() | XANTHINE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / Xanthine Dehydrogenase / FAD / molybdopterin / 2Fe-2S iron sulfur centers / salicylate | ||||||
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 | ![]() ![]() | ||||||
![]() | Enroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / Nishino, T. / Pai, E.F. | ||||||
![]() | ![]() Title: Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. Authors: Enroth, C. / Eger, B.T. / Okamoto, K. / Nishino, T. / 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 | ![]() | 562.4 KB | Display | ![]() |
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PDB format | ![]() | 447.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 696.4 KB | Display | ![]() |
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Full document | ![]() | 748.9 KB | Display | |
Data in XML | ![]() | 57.2 KB | Display | |
Data in CIF | ![]() | 95.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assmbly is a dimer constructed from a single chain in each biological monomer. The monomer is divided into 3 chains due to 2 missing loops of electron density. The dimer is generated by a two-fold. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 146993.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 8 types, 2065 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MTE.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-FES / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, DTT, glycerol, KPi, NaPPi, salicylate, EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
Crystal grow | *PLUS Method: unknown / Details: unpublished data |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.9 Å / Num. all: 176889 / Num. obs: 154198 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.387 / Num. unique all: 5988 / % possible all: 67.8 |
Reflection | *PLUS Num. obs: 7710 / Num. measured all: 154198 |
Reflection shell | *PLUS % possible obs: 67.8 % |
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Processing
Software |
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Refinement | Resolution: 2.1→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.8 Å2 |