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- PDB-2yfs: Crystal structure of inulosucrase from Lactobacillus johnsonii NC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yfs | |||||||||
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Title | Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 in complex with sucrose | |||||||||
![]() | LEVANSUCRASE | |||||||||
![]() | TRANSFERASE / FRUCTOSYLTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY GH68 / SUGAR UTILIZATION | |||||||||
Function / homology | ![]() inulosucrase / inulosucrase activity / levansucrase activity / carbohydrate utilization / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pijning, T. / Anwar, M.A. / Leemhuis, H. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
![]() | ![]() Title: Crystal Structure of Inulosucrase from Lactobacillus: Insights Into the Substrate Specificity and Product Specificity of Gh68 Fructansucrases. Authors: Pijning, T. / Anwar, M.A. / Boger, M. / Dobruchowska, J.M. / Leemhuis, H. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.6 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yfrC ![]() 2yftC ![]() 1oygS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 63852.375 Da / Num. of mol.: 1 / Fragment: RESIDUES 145-708 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Polysaccharide | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 2M (NH4)2)SO4, 5% (V/V) 2-PROPANOL, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.75 Å / Num. obs: 27086 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 60.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OYG Resolution: 2.6→38.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.534 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-175 ARE NOT VISIBLE IN ELECTRON DENSITY
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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: 44.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→38.45 Å
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Refine LS restraints |
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