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- PDB-3djd: Crystal structure of the deglycating enzyme fructosamine oxidase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3djd | ||||||
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Title | Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II) | ||||||
![]() | Fructosyl amine: oxygen oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / fructosyl-amino acid / amadoriase / deglycation / fructosamine oxidase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Collard, F. / Zhang, J. / Nemet, I. / Qanungo, K.R. / Monnier, V.M. / Yee, V.C. | ||||||
![]() | ![]() Title: Crystal structure of the deglycating enzyme fructosamine oxidase (FAOX-II) Authors: Collard, F. / Zhang, J. / Nemet, I. / Qanungo, K.R. / Monnier, V.M. / Yee, V.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.9 KB | Display | ![]() |
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PDB format | ![]() | 162.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 908.1 KB | Display | ![]() |
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Full document | ![]() | 915 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 60.7 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49429.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS THE SEQUENCE WAS VERIFIED BY SEQUENCING AND DIFFERS FROM THE UNP SEQUENCE ...ACCORDING TO THE AUTHORS THE SEQUENCE WAS VERIFIED BY SEQUENCING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1 M Hepes pH 7.4, 10 % iso-propanol, 18 % PEG 4000, protein solution 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.96 Å / Num. obs: 85107 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 12 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.925 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→36.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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