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- PDB-2yfr: Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yfr | ||||||
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Title | Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 | ||||||
![]() | 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 | ![]() | 248.2 KB | Display | ![]() |
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PDB format | ![]() | 201.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.5 KB | Display | ![]() |
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Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yfsC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63853.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 145-708 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 538 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-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: 2 M (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: ADSC CCD / Detector: CCD / Date: Feb 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→41.76 Å / Num. obs: 85480 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OYG Resolution: 1.75→121.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.201 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→121.63 Å
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Refine LS restraints |
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