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- PDB-3u2u: 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: 3u2u | |||||||||
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Title | Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and maltotetraose | |||||||||
![]() | Glycogenin-1![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / Glycogen storage disease type II (GAA) / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 235 KB | Display | ![]() |
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PDB format | ![]() | 188.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3q4sSC ![]() 3qvbC ![]() 3rmvC ![]() 3rmwC ![]() 3t7mC ![]() 3t7nC ![]() 3t7oC ![]() 3u2tC ![]() 3u2vC ![]() 3u2wC 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 / Sugars , 2 types, 4 molecules AB
#1: Protein | ![]() Mass: 29611.639 Da / Num. of mol.: 2 / Fragment: glycogenin (residues 1-262) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 5 types, 610 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-SO4 / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 2.0M Ammonium Sulphate, 0.2M Na/K tartrate, 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010 / Details: Kirkpatrick Baez bimorph mirror pair |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→45.6 Å / Num. all: 95225 / Num. obs: 95223 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.8 / Num. unique all: 13479 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3Q4S Resolution: 1.45→41.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.214 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.068 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.031 Å2
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Refine analyze | Luzzati coordinate error obs: 0.164 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→41.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 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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