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- PDB-6zn1: Trehalose transferase bound to alpha-D-glucopyranosyl-beta-galact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zn1 | ||||||
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Title | Trehalose transferase bound to alpha-D-glucopyranosyl-beta-galactopyranose from Thermoproteus uzoniensis | ||||||
![]() | Trehalose phosphorylase/synthase | ||||||
![]() | TRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bento, I. / Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.-H. / Hanefeld, U. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Anomeric Selectivity of Trehalose Transferase with Rare l-Sugars. Authors: Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 45503.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules 


#4: Sugar | ChemComp-GLC / |
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#5: Sugar | ChemComp-GIV / |
-Non-polymers , 3 types, 150 molecules 




#2: Chemical | ChemComp-SCN / #3: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.6 Details: Bis-Tris Propane, PEG 3350, potassium thiocyanide, PEG 400 |
-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: Sep 24, 2019 |
Radiation | Monochromator: DCM Oxford-FMB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→60 Å / Num. obs: 47789 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 34.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.36 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 1.568 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4717 / CC1/2: 0.69 / % possible all: 99.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: apo-Tret Resolution: 1.75→58.509 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.204 / SU B: 3.086 / SU ML: 0.096 / Average fsc free: 0.889 / Average fsc work: 0.9015 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.114 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→58.509 Å
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Refine LS restraints |
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LS refinement shell |
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