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Open data
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Basic information
Entry | Database: PDB / ID: 7ndl | ||||||||||||
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Title | Crystal structure of human GFAT-1 S205D | ||||||||||||
![]() | Isoform 2 of Glutamine-fructose-6-phosphate aminotransferase [isomerizing] 1 | ||||||||||||
![]() | TRANSFERASE / Glutamine fructose-6-phosphate amidotransferase / 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 / IRE1-mediated unfolded protein response / circadian regulation of gene expression / extracellular exosome / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ruegenberg, S. / Baumann, U. / Denzel, M.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1. Authors: Ruegenberg, S. / Mayr, F.A.M.C. / Atanassov, I. / 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 | ![]() | 752.4 KB | Display | ![]() |
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PDB format | ![]() | 639.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 44.7 KB | Display | |
Data in CIF | ![]() | 61.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zmjC ![]() 6zmkC ![]() 6r4eS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 77672.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The initial Met is post-translationally removed (confirmed by Mass spectrometry). Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q06210-2, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Chemical | #3: Chemical | ChemComp-GLU / | #4: Water | ChemComp-HOH / | Compound details | The initial Met is post-translationally removed (confirmed by Mass spectrometry). | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.99 % |
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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, 0.3 M Sodium malonate dibasic, 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-F / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9747 Å / Relative weight: 1 |
Reflection | Resolution: 2.223→90.914 Å / Num. obs: 97303 / % possible obs: 99.5 % / Redundancy: 25.8 % / Biso Wilson estimate: 59.48 Å2 / CC1/2: 1 / Net I/σ(I): 22.99 |
Reflection shell | Resolution: 2.223→2.303 Å / Num. unique obs: 9193 / CC1/2: 0.581 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6R4E Resolution: 2.223→90.914 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.82 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 288.36 Å2 / Biso mean: 87.2451 Å2 / Biso min: 36.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.223→90.914 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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