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- PDB-5uw4: Activated yeast Glycogen Synthase in complex with UDP glucosamine -

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Basic information

Entry
Database: PDB / ID: 5uw4
TitleActivated yeast Glycogen Synthase in complex with UDP glucosamine
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / Glycogen synthase / UDP-glucosamine / complex / Glycogen synthesis
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
Glycogen synthase / Glycogen synthase
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / 2-amino-2-deoxy-beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMahalingan, K.K. / Hurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: Activated state yeast Glycogen Synthase in complex with UDP glucosamine
Authors: Hurley, T.D. / Mahalingan, K.K.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
A: Glycogen [starch] synthase isoform 2
D: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,11113
Polymers327,2744
Non-polymers2,8369
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-120 kcal/mol
Surface area96130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.044, 204.698, 205.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Glycogen [starch] synthase isoform 2


Mass: 81818.617 Da / Num. of mol.: 4 / Mutation: E169Q
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) / Variant (production host): E169Q / References: UniProt: P27472, glycogen(starch) synthase
#2: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE / Glucosamine


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 - 30 % Peg 300, 0.1 M Bis-Tris pH 6.1-6.4, 25 mM G-6-P, 10 mM UDP-glucosamine
PH range: 6.1-6.4

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.03→145.5 Å / Num. obs: 78100 / % possible obs: 95.2 % / Redundancy: 4.3 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→145.16 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 21.18 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25728 4474 5.4 %RANDOM
Rwork0.18819 ---
obs0.19183 78100 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.378 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å2-0 Å2-0 Å2
2--7.4 Å20 Å2
3----4.4 Å2
Refinement stepCycle: 1 / Resolution: 2.98→145.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20196 0 176 2 20374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01920887
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218886
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.95428388
X-RAY DIFFRACTIONr_angle_other_deg1.021343634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12452542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28323.7441023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.386153367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.28115140
X-RAY DIFFRACTIONr_chiral_restr0.0840.23137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223331
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024457
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_it5.2218.4310186
X-RAY DIFFRACTIONr_mcbond_other5.228.42910185
X-RAY DIFFRACTIONr_mcangle_it8.11212.63712722
X-RAY DIFFRACTIONr_mcangle_other8.11212.63812723
X-RAY DIFFRACTIONr_scbond_it5.0538.63710701
X-RAY DIFFRACTIONr_scbond_other5.0538.63710701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.97612.86915666
X-RAY DIFFRACTIONr_long_range_B_refined11.11398.56723384
X-RAY DIFFRACTIONr_long_range_B_other11.11398.56723385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.984→3.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 295 -
Rwork0.346 5659 -
obs--97.37 %

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