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- PDB-1ll2: Crystal Structure of Rabbit Muscle Glycogenin Complexed with UDP-... -

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Basic information

Entry
Database: PDB / ID: 1ll2
TitleCrystal Structure of Rabbit Muscle Glycogenin Complexed with UDP-glucose and Manganese
ComponentsGLYCOGENIN-1
KeywordsTRANSFERASE / PROTEIN-SUBSTRATE COMPLEX / 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 / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity
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
: / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycogenin-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)38,0543
Polymers37,4331
Non-polymers6212
Water4,774265
1
A: GLYCOGENIN-1
hetero molecules

A: GLYCOGENIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1086
Polymers74,8662
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4500 Å2
ΔGint-51 kcal/mol
Surface area20930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.887, 106.875, 122.253
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-335-

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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 2, 2001 / Details: Osmic confocal optics
RadiationMonochromator: Osmic confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 29435 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.7 / Num. unique all: 29472 / % possible all: 88.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 29472 / % possible obs: 96.7 % / Num. measured all: 93616 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 88.8 % / Rmerge(I) obs: 0.372

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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
Rfree0.227 1496 4.8 %RANDOM
Rwork0.194 ---
all0.195 30315 --
obs0.195 29435 97.1 %-
Displacement parametersBiso mean: 34.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 37 265 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d23.27
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.192.5
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.923
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor all: 0.195 / Rfactor obs: 0.194 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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