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- PDB-3o3c: Glycogen synthase basal state UDP complex -

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Basic information

Entry
Database: PDB / ID: 3o3c
TitleGlycogen synthase basal state UDP complex
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / glycogen synthase
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
URIDINE-5'-DIPHOSPHATE / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.512 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
DepositionJul 23, 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 1.3Sep 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)331,12419
Polymers328,4514
Non-polymers2,67315
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-227 kcal/mol
Surface area96370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.586, 167.209, 121.251
Angle α, β, γ (deg.)90.00, 102.66, 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, YLR258W, L8479.8 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P27472, glycogen(starch) synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 20% PEG 3500, 200 mM LI2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.01 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 3.51→50 Å / Num. all: 46849 / Num. obs: 46381 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3.51-3.572.70.44492.7
3.57-3.642.90.40595.9
3.64-3.713.10.37297.1
3.71-3.783.40.32798.5
3.78-3.863.50.3198.7
3.86-3.953.60.2699.4
3.95-4.053.50.23799.7
4.05-4.163.60.299.8
4.16-4.283.60.17699.9
4.28-4.423.60.16399.9
4.42-4.583.60.14899.9
4.58-4.763.60.131100
4.76-4.983.60.12299.8
4.98-5.243.70.11899.9
5.24-5.573.70.11699.9
5.57-63.80.108100
6-6.63.80.094100
6.6-7.553.80.072100
7.55-9.513.80.059100
9.51-503.70.06599.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NAZ

3naz


Resolution: 3.512→48.288 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0 / σ(F): 1.36 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2384 5.15 %
Rwork0.2194 --
obs0.2209 46330 50.18 %
all-46849 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.342 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0952 Å20 Å26.0125 Å2
2--20.0738 Å20 Å2
3----16.9786 Å2
Refinement stepCycle: LAST / Resolution: 3.512→48.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19692 0 155 0 19847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920300
X-RAY DIFFRACTIONf_angle_d1.11427502
X-RAY DIFFRACTIONf_dihedral_angle_d19.8187340
X-RAY DIFFRACTIONf_chiral_restr0.0762984
X-RAY DIFFRACTIONf_plane_restr0.0053532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5123-3.5840.33261130.30982373X-RAY DIFFRACTION46
3.584-3.66190.30361290.29792519X-RAY DIFFRACTION49
3.6619-3.7470.26941240.27282530X-RAY DIFFRACTION49
3.747-3.84070.27751440.27462586X-RAY DIFFRACTION50
3.8407-3.94450.24991510.25552566X-RAY DIFFRACTION50
3.9445-4.06050.26991570.2482585X-RAY DIFFRACTION50
4.0605-4.19150.25211490.23462609X-RAY DIFFRACTION50
4.1915-4.34120.24871390.22622592X-RAY DIFFRACTION51
4.3412-4.51490.29121630.21332585X-RAY DIFFRACTION51
4.5149-4.72020.23751300.20672610X-RAY DIFFRACTION51
4.7202-4.96890.22131360.19022612X-RAY DIFFRACTION51
4.9689-5.27980.23741580.19822624X-RAY DIFFRACTION51
5.2798-5.68690.23581450.20312607X-RAY DIFFRACTION51
5.6869-6.25810.26611250.20992627X-RAY DIFFRACTION51
6.2581-7.16110.22121430.19022630X-RAY DIFFRACTION51
7.1611-9.01270.19171270.15982642X-RAY DIFFRACTION51
9.0127-48.29210.21421510.19052649X-RAY DIFFRACTION51

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