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Yorodumi- PDB-4ttu: N-terminally truncated dextransucrase DSR-E from Leuconostoc mese... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ttu | |||||||||
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Title | N-terminally truncated dextransucrase DSR-E from Leuconostoc mesenteroides NRRL B-1299 in complex with isomaltotriose | |||||||||
Components | Dextransucrase | |||||||||
Keywords | TRANSFERASE / alpha-1 / 2-branching-sucrase / glucan binding domain / isomaltotriose / glucansucrase | |||||||||
Function / homology | Function and homology information dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Leuconostoc mesenteroides (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | |||||||||
Authors | Brison, Y. / Remaud-Simeon, M. / Mourey, L. / Tranier, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Insights into the Carbohydrate Binding Ability of an alpha-(12) Branching Sucrase from Glycoside Hydrolase Family 70. Authors: Brison, Y. / Malbert, Y. / Czaplicki, G. / Mourey, L. / Remaud-Simeon, M. / Tranier, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ttu.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ttu.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ttu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4ttu ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4ttu | HTTPS FTP |
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-Related structure data
Related structure data | 4tvcC 4tvdC 3ttqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 123848.594 Da / Num. of mol.: 1 / Fragment: UNP residues 1759-2835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Gene: dsrE / Plasmid: pBAD Directional 102 (pBAD102) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8G9Q2, dextransucrase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose |
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#5: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 718 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-PEG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3,350, 0.1M ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→48.3 Å / Num. obs: 66927 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.18→2.3 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TTQ Resolution: 2.18→43.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.856 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.877 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→43.99 Å
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Refine LS restraints |
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