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- PDB-2wtx: Insight into the mechanism of enzymatic glycosyltransfer with ret... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wtx | ||||||
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Title | Insight into the mechanism of enzymatic glycosyltransfer with retention through the synthesis and analysis of bisubstrate glycomimetics of trehalose-6-phosphate synthase | ||||||
![]() | ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING] | ||||||
![]() | TRANSFERASE / TREHALOSE SYNTHASE / GLYCOSYLTRANSFERASE / POTASSIUM / RETENTION / STRESS RESPONSE | ||||||
Function / homology | ![]() trehalose metabolism in response to cold stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / response to osmotic stress / cellular response to heat / DNA damage response / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Errey, J.C. / Lee, S.S. / Gibson, R.P. / Martinez-Fleites, C. / Barry, C.S. / Jung, P.M.J. / OSullivan, A. / Davis, B.G. / Davies, G.J. | ||||||
![]() | ![]() Title: Mechanistic Insight Into Enzymatic Glycosyl Transfer with Retention of Configuration Through Analysis of Glycomimetic Inhibitors. Authors: Errey, J.C. / Lee, S.S. / Gibson, R.P. / Martinez Fleites, C. / Barry, C.S. / Jung, P.M.J. / O'Sullivan, A.C. / Davis, B.G. / Davies, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 379.4 KB | Display | ![]() |
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PDB format | ![]() | 310.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 72.9 KB | Display | |
Data in CIF | ![]() | 100.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gz5S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53675.973 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31677, alpha,alpha-trehalose-phosphate synthase (UDP-forming) #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-UDP / #4: Chemical | ChemComp-VDO / [( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. obs: 111567 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GZ5 Resolution: 2.2→98.91 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.365 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 29.981 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→98.91 Å
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Refine LS restraints |
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