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- PDB-3rt1: Maltodextarn bound activated state form of yeast glycogen synthas... -

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Basic information

Entry
Database: PDB / ID: 3rt1
TitleMaltodextarn bound activated state form of yeast glycogen synthase isoform 2
ComponentsPROTEIN (Glycogen [starch] synthase isoform 2)
KeywordsTRANSFERASE / Maltodextarn binding / Rossmann fold / Glycosyl transferase / Glycogen binding
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
alpha-maltotriose / alpha-maltotetraose / alpha-maltopentaose / 6-O-phosphono-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.mon_nstd_flag / _chem_comp.name / _chem_comp.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 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: PROTEIN (Glycogen [starch] synthase isoform 2)
B: PROTEIN (Glycogen [starch] synthase isoform 2)
C: PROTEIN (Glycogen [starch] synthase isoform 2)
D: PROTEIN (Glycogen [starch] synthase isoform 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,66418
Polymers328,7954
Non-polymers5,86914
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22200 Å2
ΔGint-23 kcal/mol
Surface area98930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.439, 205.328, 206.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
PROTEIN (Glycogen [starch] synthase isoform 2)


Mass: 82198.867 Da / Num. of mol.: 4 / Mutation: R589A R592A
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
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3

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Sugars , 5 types, 10 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: 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.: 1
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]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#6: 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.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Details

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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 0.1M Bis-Tris, 25% PEG 300, VAPOR DIFFUSION, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 96658 / % possible obs: 99.8 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.503 / Rsym value: 0.538 / % possible all: 99.8

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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 / Resolution: 2.8→48.58 Å / SU ML: 2.74 / σ(F): 0.04 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 4837 5 %
Rwork0.211 --
obs0.213 96658 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.12 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0268 Å20 Å2-0 Å2
2--15.3915 Å20 Å2
3----11.3647 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20618 0 333 0 20951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721458
X-RAY DIFFRACTIONf_angle_d1.01229100
X-RAY DIFFRACTIONf_dihedral_angle_d18.6557878
X-RAY DIFFRACTIONf_chiral_restr0.073230
X-RAY DIFFRACTIONf_plane_restr0.0043720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7949-2.82660.34671460.29212606X-RAY DIFFRACTION82
2.8266-2.85990.35261340.28922730X-RAY DIFFRACTION86
2.8599-2.89480.34741260.27322768X-RAY DIFFRACTION86
2.8948-2.93140.33371390.27632790X-RAY DIFFRACTION87
2.9314-2.970.30491430.27572799X-RAY DIFFRACTION87
2.97-3.01070.35541520.28012853X-RAY DIFFRACTION90
3.0107-3.05370.35141660.25882888X-RAY DIFFRACTION91
3.0537-3.09920.27921700.26372938X-RAY DIFFRACTION92
3.0992-3.14770.35041530.27052927X-RAY DIFFRACTION92
3.1477-3.19930.31351620.2713004X-RAY DIFFRACTION94
3.1993-3.25440.32631640.24823047X-RAY DIFFRACTION95
3.2544-3.31360.28691610.25523063X-RAY DIFFRACTION96
3.3136-3.37730.3271660.24553059X-RAY DIFFRACTION96
3.3773-3.44620.29321730.23663115X-RAY DIFFRACTION98
3.4462-3.52110.3061530.23463119X-RAY DIFFRACTION97
3.5211-3.6030.27731800.23343117X-RAY DIFFRACTION98
3.603-3.69310.29961660.21223149X-RAY DIFFRACTION98
3.6931-3.79290.26281540.20843179X-RAY DIFFRACTION99
3.7929-3.90450.2661810.21253143X-RAY DIFFRACTION99
3.9045-4.03040.24341830.19563172X-RAY DIFFRACTION99
4.0304-4.17440.22971630.18583209X-RAY DIFFRACTION99
4.1744-4.34140.24841690.18263188X-RAY DIFFRACTION99
4.3414-4.53890.23051710.17563188X-RAY DIFFRACTION99
4.5389-4.7780.19551750.16513231X-RAY DIFFRACTION100
4.778-5.0770.23831760.16973225X-RAY DIFFRACTION100
5.077-5.46860.22031470.17933267X-RAY DIFFRACTION100
5.4686-6.0180.24441610.18623251X-RAY DIFFRACTION100
6.018-6.88670.2211690.18283256X-RAY DIFFRACTION100
6.8867-8.66850.20971620.15593303X-RAY DIFFRACTION100
8.6685-48.58650.18071720.1673237X-RAY DIFFRACTION95

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