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- PDB-1zdg: Ser159 mutant of glycogenin complexed with UDP-glucose and manganese -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zdg | |||||||||
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Title | Ser159 mutant of glycogenin complexed with UDP-glucose and manganese | |||||||||
![]() | Glycogenin-1 | |||||||||
![]() | TRANSFERASE / glycosyltransferase | |||||||||
Function / homology | ![]() glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hurley, T.D. / Stout, S.L. / Miner, E. / Zhou, J. / Roach, P.J. | |||||||||
![]() | ![]() Title: Requirements for catalysis in mammalian glycogenin. Authors: Hurley, T.D. / Stout, S. / Miner, E. / Zhou, J. / Roach, P.J. #1: ![]() Title: The structure of the autocatalytic initiator for glycogen biosynthesis, glycogenin Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zctC ![]() 1zcuC ![]() 1zcvC ![]() 1zcyC ![]() 1zdfC ![]() 1ll3S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 39576.195 Da / Num. of mol.: 1 / Mutation: D159S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-UPG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: sodium MES, ammonium sulfate, PEG MME 5000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2003 |
Radiation | Monochromator: APS 17ID design / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33 Å / Num. all: 17291 / Num. obs: 16814 / % possible obs: 96.7 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 8.1 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.065 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible obs: 80 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 6.6 / Num. measured obs: 1381 / Χ2: 0.874 / % possible all: 81.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LL3 Resolution: 2.3→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 36.253 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.032 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Xplor file |
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