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Yorodumi- PDB-2yft: Crystal structure of inulosucrase from Lactobacillus johnsonii NC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yft | |||||||||
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Title | Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 in complex with 1-kestose | |||||||||
Components | LEVANSUCRASE | |||||||||
Keywords | TRANSFERASE / FRUCTOSYLTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY GH68 | |||||||||
Function / homology | Function and homology information inulosucrase / inulosucrase activity / levansucrase activity / carbohydrate utilization / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | LACTOBACILLUS JOHNSONII (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Pijning, T. / Anwar, M.A. / Leemhuis, H. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yft.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yft.ent.gz | 192.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/2yft ftp://data.pdbj.org/pub/pdb/validation_reports/yf/2yft | HTTPS FTP |
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-Related structure data
Related structure data | 2yfrC 2yfsC 1oygS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 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.) LACTOBACILLUS JOHNSONII (bacteria) / Strain: NCC533 / Plasmid: PETINUJ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q74K42, inulosucrase |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / 1-kestose |
-Non-polymers , 4 types, 530 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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)2SO4, 5% (V/V) 2-PROPANOL, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.89 Å / Num. obs: 72652 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 5.3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OYG Resolution: 1.85→43.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.614 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-175 AND 695-708 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: 25.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.89 Å
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Refine LS restraints |
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