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- PDB-3guh: Crystal Structure of Wild-type E.coli GS in complex with ADP and DGM -

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Basic information

Entry
Database: PDB / ID: 3guh
TitleCrystal Structure of Wild-type E.coli GS in complex with ADP and DGM
ComponentsGlycogen synthase
KeywordsTRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and intermediate D-glucopyranosylium binding / Glycogen biosynthesis / Glycosyltransferase
Function / homology
Function and homology information


starch synthase (glycosyl-transferring) / : / alpha-1,4-glucan glucosyltransferase (ADP-glucose donor) activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen biosynthetic process / DNA damage response / cytosol
Similarity search - Function
Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-250 / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / 1,5-anhydro-D-glucitol / Chem-PE3 / Glycogen synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsSheng, F. / Geiger, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Crystal Structures of the Open and Catalytically Competent Closed Conformation of Escherichia coli Glycogen Synthase.
Authors: Sheng, F. / Jia, X. / Yep, A. / Preiss, J. / Geiger, J.H.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1998
Polymers53,9511
Non-polymers2,2477
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.841, 125.841, 153.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycogen synthase / Starch [bacterial glycogen] synthase


Mass: 53951.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b3429, glgA, JW3392 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6U8, starch synthase (glycosyl-transferring)
#4: Sugar ChemComp-ASO / 1,5-anhydro-D-glucitol / 1,5-ANHYDROSORBITOL


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
D-1-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-250 / (2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid


Mass: 268.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O5S
#5: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE ASO SPECIES IN THIS PDB ENTRY DOES NOT HAVE HYDROGEN ATOM ON C1, THEREFORE IT IS POSITIVELY ...THE ASO SPECIES IN THIS PDB ENTRY DOES NOT HAVE HYDROGEN ATOM ON C1, THEREFORE IT IS POSITIVELY CHARGED AND THE PARTIAL PLANARITY IS MAINTAINED AMONG C2C1O5C5.

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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: 5.62 Å3/Da / Density % sol: 78.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 40% (w/v) PEG 4000, 0.2 M NaAc, 0.1 M HEPPSO, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→97.13 Å / Num. all: 29589 / Num. obs: 29543 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.91 / Redundancy: 8.1 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.976 / Net I/σ(I): 23.996
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.516 / Num. unique all: 2740 / Χ2: 0.511 / % possible all: 92.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.349 / Cor.coef. Fo:Fc: 0.744
Highest resolutionLowest resolution
Rotation3 Å29.93 Å
Translation3 Å29.93 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZU

1rzu


Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.861 / SU B: 7.902 / SU ML: 0.154 / SU R Cruickshank DPI: 0.287 / SU Rfree: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1478 5.1 %RANDOM
Rwork0.169 ---
obs0.17 29120 98.42 %-
all-29589 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 122.93 Å2 / Biso mean: 40.525 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 111 209 4055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213943
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.9775346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34622.849179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.50415594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5521530
X-RAY DIFFRACTIONr_chiral_restr0.1540.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213008
X-RAY DIFFRACTIONr_mcbond_it0.9451.52369
X-RAY DIFFRACTIONr_mcangle_it1.80323773
X-RAY DIFFRACTIONr_scbond_it2.74331574
X-RAY DIFFRACTIONr_scangle_it4.3114.51573
LS refinement shellResolution: 2.79→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 118 -
Rwork0.302 1694 -
all-1812 -
obs-574948 82.48 %

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