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- PDB-3u2w: Crystal Structure of Human Glycogenin-1 (GYG1) complexed with man... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u2w | ||||||
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Title | Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species | ||||||
![]() | Glycogenin-1 | ||||||
![]() | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation / glucal | ||||||
Function / homology | ![]() Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora ...Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaikuad, A. / Froese, D.S. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Yue, W.W. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis. Authors: Chaikuad, A. / Froese, D.S. / Berridge, G. / von Delft, F. / Oppermann, U. / Yue, W.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.5 KB | Display | ![]() |
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PDB format | ![]() | 184.9 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 | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q4sSC ![]() 3qvbC ![]() 3rmvC ![]() 3rmwC ![]() 3t7mC ![]() 3t7nC ![]() 3t7oC ![]() 3u2tC ![]() 3u2uC ![]() 3u2vC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29595.639 Da / Num. of mol.: 2 / Fragment: glycogenin (residues 1-262) / Mutation: Y195F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/GLC.gif)
![](data/chem/img/LCN.gif)
![](data/chem/img/LCN.gif)
#5: Sugar | #6: Sugar | ChemComp-LCN / | |
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-Non-polymers , 4 types, 511 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG 3350, 0.2M Li2(SO4), 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 24, 2011 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→22.78 Å / Num. all: 58119 / Num. obs: 58070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8458 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3Q4S Resolution: 1.68→22.585 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.496 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.672 Å2
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Refine analyze | Luzzati coordinate error obs: 0.186 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→22.585 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
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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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