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- PDB-5suk: G6P bound activated state of yeast glycogen synthase 2 -

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Basic information

Entry
Database: PDB / ID: 5suk
TitleG6P bound activated state of yeast glycogen synthase 2
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / Activated form G6P Glycogen synthase wild-type
Function / homology
Function and homology information


Glycogen synthesis / glycogen(starch) synthase / glycogen (starch) synthase activity / glycogen biosynthetic process / molecular function inhibitor activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsBaskaran, S. / Mahalingan, K.K. / Hurley, T.D.
CitationJournal: Biochemistry / Year: 2017
Title: Redox Switch for the Inhibited State of Yeast Glycogen Synthase Mimics Regulation by Phosphorylation.
Authors: Mahalingan, K.K. / Baskaran, S. / DePaoli-Roach, A.A. / Roach, P.J. / Hurley, T.D.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
C: Glycogen [starch] synthase isoform 2
D: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,04510
Polymers329,4844
Non-polymers1,5616
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-94 kcal/mol
Surface area96220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.984, 204.562, 205.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Glycogen [starch] synthase isoform 2


Mass: 82371.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GSY2, YLR258W, L8479.8 / Production host: Escherichia coli (E. coli) / References: UniProt: P27472, glycogen(starch) synthase
#2: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Peg 300, Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.88→145.09 Å / Num. obs: 84895 / % possible obs: 97.99 % / Redundancy: 5 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 21.5 / Net I/σ(I): 17.95
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.51 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NB0

3nb0


Resolution: 2.88→145.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.729 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 1.117 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26004 4461 5 %RANDOM
Rwork0.2189 ---
obs0.22098 84895 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.442 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å2-0 Å20 Å2
2--8.16 Å2-0 Å2
3----4.57 Å2
Refinement stepCycle: LAST / Resolution: 2.88→145.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19489 0 96 0 19585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01920024
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218650
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.95427243
X-RAY DIFFRACTIONr_angle_other_deg0.739342602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26452510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22923.679927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.175153129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.21815131
X-RAY DIFFRACTIONr_chiral_restr0.0560.23089
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02122923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024772
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6928.03610063
X-RAY DIFFRACTIONr_mcbond_other3.6928.03610062
X-RAY DIFFRACTIONr_mcangle_it5.87412.04612565
X-RAY DIFFRACTIONr_mcangle_other5.87412.04712566
X-RAY DIFFRACTIONr_scbond_it4.0718.0159961
X-RAY DIFFRACTIONr_scbond_other4.0718.0159961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.30311.98314679
X-RAY DIFFRACTIONr_long_range_B_refined8.78563.57222602
X-RAY DIFFRACTIONr_long_range_B_other8.78563.57222602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.883→2.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 261 -
Rwork0.321 5144 -
obs--80.91 %

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