+Open data
-Basic information
Entry | Database: PDB / ID: 6zmj | ||||||||||||
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Title | Crystal structure of human GFAT-1 R203H | ||||||||||||
Components | Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 | ||||||||||||
Keywords | TRANSFERASE / Glutamine fructose-6-phosphate amidotransferase / GFAT / Ntn hydrolase | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.774 Å | ||||||||||||
Authors | Ruegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nat Commun / Year: 2021 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. #1: Journal: Biorxiv / Year: 2020 Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1 Authors: Ruegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zmj.cif.gz | 747.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zmj.ent.gz | 637.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zmj_validation.pdf.gz | 1004.3 KB | Display | wwPDB validaton report |
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Full document | 6zmj_full_validation.pdf.gz | 1022.1 KB | Display | |
Data in XML | 6zmj_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 6zmj_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmj ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmj | HTTPS FTP |
-Related structure data
Related structure data | 6zmkC 7ndlC 6r4eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 77676.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFPT1, GFAT, GFPT / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Chemical | #3: Chemical | ChemComp-GLU / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.27 Å3/Da / Density % sol: 62.42 % |
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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 tartrae, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.774→48.653 Å / Num. obs: 49792 / % possible obs: 99.75 % / Redundancy: 13.3 % / CC1/2: 0.997 / Net I/σ(I): 14.05 |
Reflection shell | Resolution: 2.774→2.873 Å / Num. unique obs: 4773 / CC1/2: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R4E Resolution: 2.774→48.653 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.55 / 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: 419.52 Å2 / Biso mean: 104.9774 Å2 / Biso min: 29.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.774→48.653 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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