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- PDB-5sul: Inhibited state structure of yGsy2p -

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Basic information

Entry
Database: PDB / ID: 5sul
TitleInhibited state structure of yGsy2p
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / Glycogen synthase Inhibited state / Phosphorylation
Function / homology
Function and homology information


Glycogen synthesis / glycogen binding / glycogen(starch) synthase / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen granule / glycogen biosynthetic process / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMahalingan, K.K. / Hurley, T.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
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 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1264
Polymers164,3982
Non-polymers7282
Water00
1
A: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
hetero molecules

A: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,2528
Polymers328,7954
Non-polymers1,4574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10540 Å2
ΔGint-72 kcal/mol
Surface area96080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.447, 122.447, 279.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 625 / Label seq-ID: 22 - 645

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glycogen [starch] synthase isoform 2


Mass: 82198.867 Da / Num. of mol.: 2
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P

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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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Peg 6000, Magnesium Chloride, Tris-HCl / PH range: 8.5-8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.681
11-h,-k,l20.319
ReflectionResolution: 3.3→50 Å / Num. obs: 35194 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.134 / Net I/av σ(I): 10.28 / Net I/σ(I): 7.59
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.13 / CC1/2: 0.703 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NAZ

3naz


Resolution: 3.3→46.04 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.685 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22298 1896 5.1 %RANDOM
Rwork0.15797 ---
obs0.16119 35194 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.47 Å2
Baniso -1Baniso -2Baniso -3
1-13.84 Å20 Å20 Å2
2--13.84 Å20 Å2
3----27.68 Å2
Refinement stepCycle: 1 / Resolution: 3.3→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9569 0 46 0 9615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.94513411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38151219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40523.8479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.602151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9361562
X-RAY DIFFRACTIONr_chiral_restr0.1190.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217637
X-RAY DIFFRACTIONr_gen_planes_other
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_it8.75811.0834894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.08116.5956107
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.8811.0554954
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined17.90493.09815180
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 711 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.23 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.304→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 117 -
Rwork0.237 2561 -
obs--98.46 %

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