+Open data
-Basic information
Entry | Database: PDB / ID: 1ll0 | ||||||
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Title | Crystal Structure of Rabbit Muscle Glycogenin | ||||||
Components | GLYCOGENIN-1 | ||||||
Keywords | TRANSFERASE / beta-alpha-beta Rossman-like nucleotide binding fold / DxD motif | ||||||
Function / homology | Function and homology information glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.43 Å | ||||||
Authors | Gibbons, B.J. / Roach, P.J. / Hurley, T.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin. Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ll0.cif.gz | 465.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ll0.ent.gz | 389.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ll0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ll0_validation.pdf.gz | 545.3 KB | Display | wwPDB validaton report |
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Full document | 1ll0_full_validation.pdf.gz | 680.1 KB | Display | |
Data in XML | 1ll0_validation.xml.gz | 104.4 KB | Display | |
Data in CIF | 1ll0_validation.cif.gz | 134.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/1ll0 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/1ll0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38068.570 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P13280, glycogenin glucosyltransferase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.73 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 8-10 mg/mL glycogenin, 0.7 to 1.2 M ammonium sulphate, and 100 mM sodium phosphate buffer pH 6.6 to 6.9, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / PH range low: 6.9 / PH range high: 6.6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9794, 0.9322 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 1, 2000 / Details: Rosenbaum-Rock monochromators and focusing mirror | ||||||||||||
Radiation | Monochromator: Monochromator 1: sagittal focusing Si(220)/Monochromator 2: sagittal focusing Si (111) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.43→50 Å / Num. obs: 56152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.088 / Net I/σ(I): 26 | ||||||||||||
Reflection shell | Resolution: 3.43→3.52 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4.2 / Num. unique all: 56152 / % possible all: 99.3 | ||||||||||||
Reflection | *PLUS Num. measured all: 403861 / Rmerge(I) obs: 0.088 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.484 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.43→25 Å / σ(F): 0.5 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 79.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.43→25 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.43 Å / Lowest resolution: 25 Å / Rfactor all: 0.254 / Rfactor obs: 0.252 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.252 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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