+
Open data
-
Basic information
Entry | Database: PDB / ID: 3q4s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Glycogenin-1 (GYG1), apo form | ||||||
![]() | Glycogenin-1 | ||||||
![]() | TRANSFERASE / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaikuad, A. / Froese, D.S. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, O. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 119.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3qvbC ![]() 3rmvC ![]() 3rmwC ![]() 3t7mC ![]() 3t7nC ![]() 3t7oC ![]() 3u2tC ![]() 3u2uC ![]() 3u2vC ![]() 3u2wC ![]() 1ll3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 29595.639 Da / Num. of mol.: 1 / Fragment: glycogenin (residues 1-262) / Mutation: Y195F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG smears (PEG 2000, 3350, 4000, 5000MME), 0.1M PIPES, pH 7.0, 0.1M MgCl2, 0.1M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2010 |
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: 1.98→30.04 Å / Num. all: 19979 / Num. obs: 19954 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2 / Num. unique all: 2784 / % possible all: 94.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb id 1LL3 Resolution: 1.98→29.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.12 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IN REFINEMENT BUT NOT OUTPUT TO PDB
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.295 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.227 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→29.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|