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- PDB-3rsz: Maltodextran bound basal state conformation of yeast glycogen syn... -

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Basic information

Entry
Database: PDB / ID: 3rsz
TitleMaltodextran bound basal state conformation of yeast glycogen synthase isoform 2
Components(Glycogen [starch] synthase isoform 2) x 2
KeywordsTRANSFERASE / Maltodextran Binding / Rossmann fold / Glycosyl transferase / Glycogen binding
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
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
alpha-maltotetraose / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.009 Å
AuthorsBaskaran, S. / Hurley, T.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Multiple Glycogen-binding Sites in Eukaryotic Glycogen Synthase Are Required for High Catalytic Efficiency toward Glycogen.
Authors: Baskaran, S. / Chikwana, V.M. / Contreras, C.J. / Davis, K.D. / Wilson, W.A. / Depaoli-Roach, A.A. / Roach, P.J. / Hurley, T.D.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
E: Glycogen [starch] synthase isoform 2
F: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,54126
Polymers329,3386
Non-polymers4,20320
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17760 Å2
ΔGint-224 kcal/mol
Surface area96430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.557, 166.731, 121.136
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:204 or resseq 207:276 or resseq...
211chain B and (resseq 1:204 or resseq 207:276 or resseq...
112chain C and (resseq 1:204 or resseq 207:276 or resseq...
212chain D and (resseq 1:204 or resseq 207:276 or resseq...
113chain A and (resseq 1:204 or resseq 207:276 or resseq...
213chain B and (resseq 1:204 or resseq 207:276 or resseq...
114chain C and (resseq 1:204 or resseq 207:276 or resseq...
214chain D and (resseq 1:204 or resseq 207:276 or resseq...

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly for the main polymeric chain is a tetramer

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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 Glycogen [starch] synthase isoform 2


Mass: 443.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET28A / Production host: Escherichia coli (E. coli)
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
Sequence detailsAUTHORS SEQUENCE MATCHES WITH GENBANK ENTRY CODE AAA88716. SEE SEQADV REMARK

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3400, 0.1M Lithium Sulfate, 0.1M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 77170 / Num. obs: 73079 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.082 / Rsym value: 0.075 / Net I/σ(I): 13.2
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2 / Rsym value: 0.449

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3NAZ

3naz


Resolution: 3.009→47.564 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 3673 5.03 %
Rwork0.2066 --
obs0.2084 73079 98.85 %
all-77170 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.464 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1912 Å20 Å24.9799 Å2
2--4.1823 Å2-0 Å2
3----12.3735 Å2
Refinement stepCycle: LAST / Resolution: 3.009→47.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19751 0 260 0 20011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820465
X-RAY DIFFRACTIONf_angle_d1.15227731
X-RAY DIFFRACTIONf_dihedral_angle_d17.2547545
X-RAY DIFFRACTIONf_chiral_restr0.0823057
X-RAY DIFFRACTIONf_plane_restr0.0043539
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2424X-RAY DIFFRACTIONPOSITIONAL
12B2424X-RAY DIFFRACTIONPOSITIONAL0.031
21C2432X-RAY DIFFRACTIONPOSITIONAL
22D2432X-RAY DIFFRACTIONPOSITIONAL0.032
31A2466X-RAY DIFFRACTIONPOSITIONAL
32B2466X-RAY DIFFRACTIONPOSITIONAL0.01
41C2470X-RAY DIFFRACTIONPOSITIONAL
42D2470X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0092-3.04880.38131100.3442205X-RAY DIFFRACTION82
3.0488-3.09050.35391290.30592601X-RAY DIFFRACTION97
3.0905-3.13470.30621340.31422643X-RAY DIFFRACTION98
3.1347-3.18150.33171320.28382714X-RAY DIFFRACTION100
3.1815-3.23120.33291230.28972722X-RAY DIFFRACTION100
3.2312-3.28410.28011230.26512677X-RAY DIFFRACTION100
3.2841-3.34070.31131290.25922719X-RAY DIFFRACTION100
3.3407-3.40150.25821440.25962661X-RAY DIFFRACTION100
3.4015-3.46690.29911470.24112703X-RAY DIFFRACTION100
3.4669-3.53760.26381520.24552666X-RAY DIFFRACTION100
3.5376-3.61450.23681430.23262672X-RAY DIFFRACTION100
3.6145-3.69860.2761360.2222746X-RAY DIFFRACTION100
3.6986-3.7910.2331450.21342684X-RAY DIFFRACTION100
3.791-3.89350.22351440.20622687X-RAY DIFFRACTION100
3.8935-4.0080.23411580.2032662X-RAY DIFFRACTION100
4.008-4.13730.23281620.19532678X-RAY DIFFRACTION100
4.1373-4.28510.21931480.18172710X-RAY DIFFRACTION100
4.2851-4.45650.2321600.17982654X-RAY DIFFRACTION100
4.4565-4.65920.20381320.16862735X-RAY DIFFRACTION100
4.6592-4.90460.20111550.16942702X-RAY DIFFRACTION100
4.9046-5.21150.20141530.17752685X-RAY DIFFRACTION100
5.2115-5.61330.24551470.2042689X-RAY DIFFRACTION100
5.6133-6.17710.28161360.22342718X-RAY DIFFRACTION100
6.1771-7.06850.24951500.19482709X-RAY DIFFRACTION100
7.0685-8.8960.20671250.16242747X-RAY DIFFRACTION100
8.896-47.56990.24531560.20142617X-RAY DIFFRACTION95

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