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- PDB-3nch: Yeast Glycogen Synthase (Gsy2p) Basal State Conformation -

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Basic information

Entry
Database: PDB / ID: 3nch
TitleYeast Glycogen Synthase (Gsy2p) Basal State Conformation
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / Glycogen Synthase / allosteric activation / glucose-6-phosphate
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 / MOLECULAR REPLACEMENT / Resolution: 2.88 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 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,89219
Polymers328,4514
Non-polymers1,44115
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-269 kcal/mol
Surface area97060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.940, 161.837, 121.622
Angle α, β, γ (deg.)90.00, 95.82, 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ...THE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ANNOTATED IN GENBANK ENTRY ACCESSION CODE AAA88716

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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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M Lithium sulfate, 20% PEG 3400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.01 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. all: 81200 / Num. obs: 80388 / % possible obs: 99 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 4.7 % / Biso Wilson estimate: 69.75 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NAZ

3naz


Resolution: 2.88→46.728 Å / SU ML: 1.1 / σ(F): 1.94 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 4041 5.03 %Random
Rwork0.2127 ---
obs0.2154 80301 99 %-
all-81200 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.917 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.0629 Å2-0 Å29.8096 Å2
2--1.0624 Å20 Å2
3----14.1253 Å2
Refinement stepCycle: LAST / Resolution: 2.88→46.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19712 0 75 0 19787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820232
X-RAY DIFFRACTIONf_angle_d1.14227392
X-RAY DIFFRACTIONf_dihedral_angle_d19.8247298
X-RAY DIFFRACTIONf_chiral_restr0.0832969
X-RAY DIFFRACTIONf_plane_restr0.0053533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8799-2.91370.37241160.30032088X-RAY DIFFRACTION40
2.9137-2.94930.36071300.29622628X-RAY DIFFRACTION50
2.9493-2.98660.33411310.29292653X-RAY DIFFRACTION50
2.9866-3.02590.35091300.28222644X-RAY DIFFRACTION50
3.0259-3.06730.34831380.28252626X-RAY DIFFRACTION50
3.0673-3.11110.31451420.26992643X-RAY DIFFRACTION50
3.1111-3.15760.33891250.26772626X-RAY DIFFRACTION50
3.1576-3.20690.3191380.26672628X-RAY DIFFRACTION50
3.2069-3.25950.31781250.25822646X-RAY DIFFRACTION50
3.2595-3.31570.27981480.25882637X-RAY DIFFRACTION50
3.3157-3.37590.29341350.24882649X-RAY DIFFRACTION50
3.3759-3.44080.30781490.24142627X-RAY DIFFRACTION50
3.4408-3.51110.29571220.23582672X-RAY DIFFRACTION50
3.5111-3.58740.27221370.22772632X-RAY DIFFRACTION50
3.5874-3.67080.30441580.20812626X-RAY DIFFRACTION50
3.6708-3.76260.27451240.20782675X-RAY DIFFRACTION50
3.7626-3.86420.23711470.19632600X-RAY DIFFRACTION50
3.8642-3.97790.2291660.20192656X-RAY DIFFRACTION50
3.9779-4.10620.23451360.20232646X-RAY DIFFRACTION50
4.1062-4.25290.26041640.19112652X-RAY DIFFRACTION50
4.2529-4.4230.29041390.19042642X-RAY DIFFRACTION50
4.423-4.62420.23841390.1862666X-RAY DIFFRACTION50
4.6242-4.86770.21361390.16522680X-RAY DIFFRACTION50
4.8677-5.17230.21641650.17192633X-RAY DIFFRACTION51
5.1723-5.57110.24531360.18812674X-RAY DIFFRACTION51
5.5711-6.13060.28341400.19922666X-RAY DIFFRACTION51
6.1306-7.01520.24531380.18662681X-RAY DIFFRACTION51
7.0152-8.82860.21621310.15832704X-RAY DIFFRACTION51
8.8286-46.7340.19251530.18362660X-RAY DIFFRACTION50

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