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Yorodumi- PDB-3tto: Crystal structure of Leuconostoc mesenteroides NRRL B-1299 N-term... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tto | ||||||
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Title | Crystal structure of Leuconostoc mesenteroides NRRL B-1299 N-terminally truncated dextransucrase DSR-E in triclinic form | ||||||
Components | Dextransucrase | ||||||
Keywords | TRANSFERASE / (beta/alpha)8 barrel / sucrose/dextran/gluco-oligosaccharide binding / alpha-1 / 2 branching dextransucrase | ||||||
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: 3.3 Å | ||||||
Authors | Brison, Y. / Pijning, T. / Fabre, E. / Mourey, L. / Morel, S. / Potocki-Veronese, G. / Monsan, P. / Tranier, S. / Remaud-Simeon, M. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Functional and structural characterization of alpha-(1-2) branching sucrase derived from DSR-E glucansucrase Authors: Brison, Y. / Pijning, T. / Malbert, Y. / Fabre, E. / Mourey, L. / Morel, S. / Potocki-Veronese, G. / Monsan, P. / Tranier, S. / Remaud-Simeon, M. / 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 | 3tto.cif.gz | 806.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tto.ent.gz | 640.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/3tto ftp://data.pdbj.org/pub/pdb/validation_reports/tt/3tto | HTTPS FTP |
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-Related structure data
Related structure data | 3ttqC 3klkS 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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Unit cell |
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-Components
#1: Protein | Mass: 123470.891 Da / Num. of mol.: 4 Fragment: N-terminally truncated DSR-E, UniProt residues 1759-2835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Strain: NRRL B-1299 / Gene: dsr-E, dsrE / Plasmid: pBAD Directional 102 (pBAD102) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8G9Q2, dextransucrase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.96 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 17% PEG 3350, 0.2 M ammonium iodide, 80 mM ammonium citrate, 2% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→51.62 Å / Num. all: 82750 / Num. obs: 80648 / % possible obs: 97.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 42.3 Å2 / Rsym value: 0.203 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 3.3→3.48 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.533 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KLK Resolution: 3.3→51.62 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.758 / SU B: 33.4 / SU ML: 0.537 / Cross valid method: THROUGHOUT / ESU R Free: 0.642 / 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: 27.267 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→51.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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