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- PDB-5zkw: Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zkw | |||||||||
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Title | Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with GF2 | |||||||||
![]() | 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 | ![]() | 499.5 KB | Display | ![]() |
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PDB format | ![]() | 408.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 95.6 KB | Display | |
Data in CIF | ![]() | 141 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zksC ![]() 5zkuC ![]() 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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1 | ![]()
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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: Polysaccharide | alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350,0.1 M Sodium malonate (pH 4.2) |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.86→50 Å / Num. obs: 209495 / % possible obs: 99.2 % / Redundancy: 5.4 % / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.86→1.89 Å |
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Processing
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Refinement | Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.794 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.118 / 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: 27.728 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→50 Å
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Refine LS restraints |
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