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- PDB-3v8z: Structure of apo-glycogenin truncated at residue 270 complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v8z | ||||||
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Title | Structure of apo-glycogenin truncated at residue 270 complexed with UDP | ||||||
![]() | Glycogenin-1 | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A. | ||||||
![]() | ![]() Title: Structural and biochemical insight into glycogenin inactivation by the glycogenosis-causing T82M mutation. Authors: Carrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.6 KB | Display | ![]() |
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Full document | ![]() | 791.4 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32607.670 Da / Num. of mol.: 1 / Fragment: UNP residues 1-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 135 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-UDP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 1.0 M ammonium sulfate/0.1 M sodium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2010 / Details: Mirrors |
Radiation | Monochromator: Silicium curved crystal, with asymmetric 7.25 angle cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25.74 Å / Num. all: 18783 / Num. obs: 18783 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2687 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 19.638 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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