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- PDB-6r4j: Crystal structure of human GFAT-1 G451E in complex with UDP-GlcNAc -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r4j | |||||||||
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Title | Crystal structure of human GFAT-1 G451E in complex with UDP-GlcNAc | |||||||||
![]() | Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 | |||||||||
![]() | TRANSFERASE / Glutamine fructose-6-phosphate aminotransferase / GFAT / Ntn hydrolase | |||||||||
Function / homology | ![]() Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process ...Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / circadian regulation of gene expression / extracellular exosome / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ruegenberg, S. / Horn, M. / Pichlo, C. / Allmeroth, K. / Baumann, U. / Denzel, M.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis. Authors: Ruegenberg, S. / Horn, M. / Pichlo, C. / Allmeroth, K. / Baumann, U. / Denzel, M.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 | ![]() | 745.8 KB | Display | ![]() |
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PDB format | ![]() | 628.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 62.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r4eSC ![]() 6r4fC ![]() 6r4gC ![]() 6r4hC ![]() 6r4iC ![]() 6svmC ![]() 6svoC ![]() 6svpC ![]() 6svqC 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, 2 molecules AB
#1: Protein | Mass: 77768.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing) |
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-Non-polymers , 5 types, 133 molecules ![](data/chem/img/UD1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G6Q.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G6Q.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GLU / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis tris propane pH 9.0, 0.4 M Potassium sodium tartrate, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→48.73 Å / Num. obs: 74011 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 18.36 |
Reflection shell | Resolution: 2.42→2.51 Å / Num. unique obs: 7226 / CC1/2: 0.599 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6R4E Resolution: 2.42→48.727 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→48.727 Å
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Refine LS restraints |
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LS refinement shell |
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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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