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- PDB-6svo: Crystal structure of human GFAT-1 in complex with Glucosamine-6-P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6svo | ||||||||||||
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Title | Crystal structure of human GFAT-1 in complex with Glucosamine-6-Phosphate and L-Glu | ||||||||||||
![]() | 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 | ![]() | 756.5 KB | Display | ![]() |
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PDB format | ![]() | 644.3 KB | 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 | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r4eSC ![]() 6r4fC ![]() 6r4gC ![]() 6r4hC ![]() 6r4iC ![]() 6r4jC ![]() 6svmC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 77775.984 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) #2: Chemical | #3: Chemical | ChemComp-GLU / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis tris propane pH 8.75, 0.2 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 6M / Detector: PIXEL / Date: Aug 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.328→48.335 Å / Num. obs: 84017 / % possible obs: 99.8 % / Redundancy: 22.3 % / CC1/2: 0.999 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.33→2.41 Å / Num. unique obs: 8181 / CC1/2: 0.558 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6R4E Resolution: 2.328→48.335 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 307.6 Å2 / Biso mean: 98.1629 Å2 / Biso min: 40.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.328→48.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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