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Open data
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Basic information
Entry | Database: PDB / ID: 6t1p | |||||||||
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Title | ASR Alternansucrase in complex with isomaltononaose | |||||||||
![]() | Alternansucrase | |||||||||
![]() | TRANSFERASE / glucansucrase / polysaccharides / dextran / alternan / GH70 / sucrose | |||||||||
Function / homology | ![]() dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cioci, G. / Molina, M. / Moulis, C. / Remaud-Simeon, M. | |||||||||
![]() | ![]() Title: A specific oligosaccharide-binding site in the alternansucrase catalytic domain mediates alternan elongation. Authors: Molina, M. / Moulis, C. / Monties, N. / Guieysse, D. / Morel, S. / Cioci, G. / Remaud-Simeon, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 981.5 KB | Display | ![]() |
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PDB format | ![]() | 806.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 78.5 KB | Display | |
Data in CIF | ![]() | 107.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6syqC ![]() 6sziC ![]() 6t16C ![]() 6t18C ![]() 6hvgS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 239 - 1423 / Label seq-ID: 93 - 1277
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Components
#1: Protein | Mass: 142581.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350 14% 0.4M NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→118.6 Å / Num. obs: 39240 / % possible obs: 94.9 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3.5→3.69 Å / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1 / Num. unique obs: 4793 / CC1/2: 0.712 / % possible all: 80.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6hvg Resolution: 3.5→118.6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 89.203 / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.695 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 235.14 Å2 / Biso mean: 108.285 Å2 / Biso min: 64.64 Å2
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Refinement step | Cycle: final / Resolution: 3.5→118.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7864 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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