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- PDB-3naz: Basal state form of Yeast Glycogen Synthase -

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Basic information

Entry
Database: PDB / ID: 3naz
TitleBasal state form of Yeast Glycogen Synthase
Components
  • Glycogen [starch] synthase isoform 2
  • PEPTIDE
KeywordsTRANSFERASE / Glycogen Synthase / Glucose-6-phosphate / Yeast / Allosteric activation
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
F1FO ATP Synthase / F1FO ATP Synthase - #10 / Glycogen synthase / Glycogen synthase / Glycogen Phosphorylase B; / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsBaskaran, S. / Hurley, T.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for glucose-6-phosphate activation of glycogen synthase.
Authors: Baskaran, S. / Roach, P.J. / Depaoli-Roach, A.A. / Hurley, T.D.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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
E: PEPTIDE
F: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,04522
Polymers329,5086
Non-polymers1,53716
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-256 kcal/mol
Surface area97010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.529, 166.154, 121.029
Angle α, β, γ (deg.)90.00, 103.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycogen [starch] synthase isoform 2


Mass: 82112.750 Da / Num. of mol.: 4 / Mutation: R580A, R581A, R583A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSY2, L8479.8, YLR258W / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P27472, glycogen(starch) synthase
#2: Protein/peptide PEPTIDE


Mass: 528.644 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSY2, L8479.8, YLR258W / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
Sequence details1) THE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ...1) THE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ANNOTATED IN GENBANK ENTRY ACCESSION CODE AAA88716. 2) CHAINS E AND F HAVE POOR ELECTRON DENSITY. THEY COULD BE EITHER A SEGMENT OF THE C-TERMINAL DISORDER REGION (RESIDUES 642-705) OR THE N-TERMINAL HIS-TAG FROM SYMMETRY RELATED MOLECULE.

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 20% PEG 3400, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 73853 / % possible obs: 99.6 % / Observed criterion σ(I): 0.2 / Redundancy: 3.7 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 3→48.03 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 2.44 / Isotropic thermal model: Isotropic / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 3566 5.05 %
Rwork0.203 --
obs0.205 70557 94.8 %
all-74411 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.8 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 64.47 Å2
Baniso -1Baniso -2Baniso -3
1-3.234 Å20 Å22.486 Å2
2--6.737 Å20 Å2
3----9.971 Å2
Refinement stepCycle: LAST / Resolution: 3→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19771 0 80 0 19851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820292
X-RAY DIFFRACTIONf_angle_d1.06827473
X-RAY DIFFRACTIONf_dihedral_angle_d19.1227308
X-RAY DIFFRACTIONf_chiral_restr0.0762980
X-RAY DIFFRACTIONf_plane_restr0.0043543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0390.3841140.3222041X-RAY DIFFRACTION72
3.039-3.0820.3491150.2982329X-RAY DIFFRACTION83
3.082-3.1280.3151250.2822429X-RAY DIFFRACTION85
3.128-3.1770.3421200.2742468X-RAY DIFFRACTION88
3.177-3.2290.3161140.2752584X-RAY DIFFRACTION90
3.229-3.2850.3111230.2612519X-RAY DIFFRACTION90
3.285-3.3440.3051280.2482643X-RAY DIFFRACTION92
3.344-3.4090.2871380.2352649X-RAY DIFFRACTION94
3.409-3.4780.2771600.2292629X-RAY DIFFRACTION95
3.478-3.5540.2721390.2272736X-RAY DIFFRACTION96
3.554-3.6360.2471390.2142711X-RAY DIFFRACTION96
3.636-3.7270.2381410.2062745X-RAY DIFFRACTION98
3.727-3.8280.2521520.2082727X-RAY DIFFRACTION98
3.828-3.9410.2621620.1982770X-RAY DIFFRACTION98
3.941-4.0680.2271660.1882771X-RAY DIFFRACTION99
4.068-4.2130.2141610.1792784X-RAY DIFFRACTION99
4.213-4.3820.2551610.182826X-RAY DIFFRACTION99
4.382-4.5810.2521540.1722793X-RAY DIFFRACTION100
4.581-4.8220.1871550.1612813X-RAY DIFFRACTION100
4.822-5.1240.2151490.1622828X-RAY DIFFRACTION100
5.124-5.5190.231570.1782810X-RAY DIFFRACTION99
5.519-6.0740.2951420.1972830X-RAY DIFFRACTION99
6.074-6.950.2411560.1912828X-RAY DIFFRACTION100
6.95-8.7480.2251300.162877X-RAY DIFFRACTION100
8.748-48.0390.2281650.1812851X-RAY DIFFRACTION99

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