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- PDB-2r4t: Crystal Structure of Wild-type E.coli GS in Complex with ADP and ... -

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Basic information

Entry
Database: PDB / ID: 2r4t
TitleCrystal Structure of Wild-type E.coli GS in Complex with ADP and Glucose(wtGSc)
ComponentsGlycogen synthase
KeywordsTRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and glucose binding
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 / ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / Chem-PE3 / Glycogen synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.258 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
DepositionSep 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.4Aug 30, 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)63,07917
Polymers53,9511
Non-polymers9,12716
Water6,035335
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.827, 126.827, 151.869
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 / E.C.2.4.1.21 / 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: glgA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6U8, starch synthase (glycosyl-transferring)
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 350 molecules

#3: 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
#4: 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.: 13 / Source method: obtained synthetically / Formula: C28H58O15
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 5.7 Å3/Da / Density % sol: 78.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 40%(w/v) PEG 4000, 0.2 M Na tartrate and 0.1 M HEPPSO (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2006
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.258→97.13 Å / Num. obs: 56077 / % possible obs: 99.9 % / Observed criterion σ(I): 4.5 / Redundancy: 5.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.001 / Net I/σ(I): 11.8
Reflection shellResolution: 2.258→2.34 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5555 / Χ2: 0.635 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.306 / Cor.coef. Fo:Fc: 0.77
Highest resolutionLowest resolution
Rotation3 Å40.73 Å
Translation3 Å40.73 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZS

2qzs


Resolution: 2.258→97.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.944 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(I): 4.5 / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2845 5.1 %RANDOM
Rwork0.163 ---
all0.182 ---
obs0.1631 56062 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.998 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.258→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 150 335 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213977
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9815373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09222.849179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5281530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023000
X-RAY DIFFRACTIONr_nbd_refined0.2330.31922
X-RAY DIFFRACTIONr_nbtor_refined0.3250.52673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5550
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.529
X-RAY DIFFRACTIONr_mcbond_it0.78622427
X-RAY DIFFRACTIONr_mcangle_it1.33133775
X-RAY DIFFRACTIONr_scbond_it0.77221771
X-RAY DIFFRACTIONr_scangle_it1.0931597
LS refinement shellResolution: 2.258→2.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 188 -
Rwork0.207 3870 -
all-4058 -
obs-5555 98.57 %

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