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- PDB-1ll3: Crystal Structure of Rabbit Muscle Glycogenin -

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Basic information

Entry
Database: PDB / ID: 1ll3
TitleCrystal Structure of Rabbit Muscle Glycogenin
ComponentsGLYCOGENIN-1
KeywordsTRANSFERASE / autocatalytic initiator of glycogen biosynthesis / glycogenin / retaining glycosyltransferase - family 8 / beta-alpha-beta Rossman-like nucleotide binding fold / DxD motif / non-proline cis peptide bond
Function / homology
Function and homology information


glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
: / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGibbons, B.J. / Roach, P.J. / Hurley, T.D.
CitationJournal: 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
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGENIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6173
Polymers37,4331
Non-polymers1842
Water4,414245
1
A: GLYCOGENIN-1
hetero molecules

A: GLYCOGENIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2346
Polymers74,8662
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3660 Å2
ΔGint-26 kcal/mol
Surface area21670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.129, 104.830, 120.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-455-

HOH

DetailsThe asymetric unit contains one monomer. To construct the dimer apply the following symmetry operations: matrix:(-1.00000 -0.00001 0.00002)(0.00001 -1.00000 0.00002)(0.00002 0.00002 1.00000) translation:(-0.00052 -106.87773 0.00065)

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Components

#1: Protein GLYCOGENIN-1


Mass: 37432.852 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
18-10 mg/mlglycogenin1reservoir
20.7-1.2 Mammonium sulfate1reservoir
3100 mMsodium phosphate1reservoirpH6.6-6.9

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.079
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.079 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 29958 / Num. obs: 29664 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.4 / Num. unique all: 29807 / % possible all: 92.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 29807 / % possible obs: 98.4 % / Num. measured all: 162821 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 92.9 % / Rmerge(I) obs: 0.559

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1487 -RANDOM
Rwork0.21 ---
all0.211 29958 --
obs0.211 29664 99 %-
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--18.635 Å2--
2--8.668 Å2-
3---9.967 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 12 245 2329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d23.42
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it0
X-RAY DIFFRACTIONc_mcangle_it0
X-RAY DIFFRACTIONc_scbond_it0
X-RAY DIFFRACTIONc_scangle_it0
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.212 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.42
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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