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- PDB-4tvd: N-terminally truncated dextransucrase DSR-E from Leuconostoc mese... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tvd | ||||||
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Title | N-terminally truncated dextransucrase DSR-E from Leuconostoc mesenteroides NRRL B-1299 in complex with D-glucose | ||||||
![]() | Dextransucrase | ||||||
![]() | TRANSFERASE / alpha-1 / 2-branching-sucrase / glucan-binding domain / glucansucrase / D-glucose | ||||||
Function / homology | ![]() dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brison, Y. / Remaud-Simeon, M. / Mourey, L. / Tranier, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.4 KB | Display | ![]() |
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PDB format | ![]() | 178.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.1 KB | Display | ![]() |
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Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ttuC ![]() 4tvcC ![]() 3ttqS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 124100.375 Da / Num. of mol.: 1 Fragment: alpha-1,2 branching sucrase UNP Residues 1759-2835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dsr-E / Plasmid: pBad / Details (production host): pBAD Directional 102 (pBAD102) / Production host: ![]() ![]() References: UniProt: Q8G9Q2, UniProt: G8XR50*PLUS, dextransucrase |
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-Sugars , 2 types, 10 molecules ![](data/chem/img/BGC.gif)
![](data/chem/img/GLC.gif)
![](data/chem/img/GLC.gif)
#3: Sugar | ChemComp-BGC / #4: Sugar | ChemComp-GLC / | |
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-Non-polymers , 3 types, 397 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.1 M ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.75 Å / Num. obs: 54664 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TTQ Resolution: 2.3→47.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.94 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.214 / 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: 39.772 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→47.7 Å
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Refine LS restraints |
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