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Yorodumi- PDB-2wtx: Insight into the mechanism of enzymatic glycosyltransfer with ret... -
+Open data
-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 | ||||||
Components | ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING] | ||||||
Keywords | TRANSFERASE / TREHALOSE SYNTHASE / GLYCOSYLTRANSFERASE / POTASSIUM / RETENTION / STRESS RESPONSE | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wtx.cif.gz | 379.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wtx.ent.gz | 310.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/2wtx ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wtx | HTTPS FTP |
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-Related structure data
Related structure data | 1gz5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9791 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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