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- PDB-5zku: Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zku | ||||||
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Title | Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with DFA-III | ||||||
![]() | DFA-IIIase | ||||||
![]() | HYDROLASE / hydrolyze difructose anhydride / parallel beta helix / endoenzyme | ||||||
Function / homology | ![]() inulin fructotransferase (DFA-I-forming) / inulin fructotransferase (DFA-I-forming) activity / transferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Yu, S.H. / Shen, H. / Li, X. / Mu, W.M. | ||||||
![]() | ![]() Title: Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue Authors: Yu, S.H. / Shen, H. / Cheng, Y.Y. / Zhu, Y.Y. / Li, X. / Mu, W.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 488.8 KB | Display | ![]() |
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PDB format | ![]() | 403.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zksC ![]() 5zkwC ![]() 5zkyC ![]() 5zl4C ![]() 5zl5C ![]() 5zlaC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47197.953 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Achl_2895 Production host: ![]() ![]() References: UniProt: B8HDZ1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-9F3 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 0.1M Sodium malonate (pH 4.2) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 92637 / % possible obs: 91.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.32→2.36 Å / Rmerge(I) obs: 0.361 |
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Processing
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Refinement | Resolution: 2.32→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.141 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.691 / ESU R Free: 0.279 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.825 Å2
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Refinement step | Cycle: 1 / Resolution: 2.32→50 Å
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Refine LS restraints |
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