[English] 日本語
Yorodumi- PDB-1zdg: Ser159 mutant of glycogenin complexed with UDP-glucose and manganese -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zdg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ser159 mutant of glycogenin complexed with UDP-glucose and manganese | |||||||||
Components | Glycogenin-1 | |||||||||
Keywords | TRANSFERASE / glycosyltransferase | |||||||||
Function / homology | Function and homology information glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Hurley, T.D. / Stout, S.L. / Miner, E. / Zhou, J. / Roach, P.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Requirements for catalysis in mammalian glycogenin. Authors: Hurley, T.D. / Stout, S. / Miner, E. / Zhou, J. / Roach, P.J. #1: Journal: J.Mol.Biol. / Year: 2002 Title: The structure of the autocatalytic initiator for glycogen biosynthesis, glycogenin Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zdg.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zdg.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zdg ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zdg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zctC 1zcuC 1zcvC 1zcyC 1zdfC 1ll3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 39576.195 Da / Num. of mol.: 1 / Mutation: D159S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GYG, GYG1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: P13280, glycogenin glucosyltransferase |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-UPG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.5 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 36.253 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.032 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|