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- PDB-3cop: Crystal Structure of E.coli GS mutant E377A in complex with ADP a... -

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Basic information

Entry
Database: PDB / ID: 3cop
TitleCrystal Structure of E.coli GS mutant E377A in complex with ADP and acceptor analogue HEPPSO
ComponentsGlycogen synthase
KeywordsTRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP / acceptor analogue HEPPSO binding / Glycogen biosynthesis / Glycosyltransferase
Function / homology
Function and homology information


starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / glycogen (starch) synthase 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 / Glycogen synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSheng, F. / Geiger, J.H.
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 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: 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 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,7694
Polymers53,8931
Non-polymers8763
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.840, 125.840, 151.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 53893.312 Da / Num. of mol.: 1 / Mutation: E377A
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 / 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
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% (w/v) PEG 4000, 0.1 M HEPPSO, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.03 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48231 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2 / Num. unique all: 6111 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.356 / Cor.coef. Fo:Fc: 0.712
Highest resolutionLowest resolution
Rotation3 Å34.94 Å
Translation3 Å34.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QZS

2qzs


Resolution: 2.3→34.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.037 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2452 5.1 %RANDOM
Rwork0.174 ---
obs0.175 48150 92.56 %-
all-52053 --
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: 44.487 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 56 298 4103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213911
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9675331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.97722.802182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40215596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4931531
X-RAY DIFFRACTIONr_chiral_restr0.0870.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023023
X-RAY DIFFRACTIONr_nbd_refined0.220.31939
X-RAY DIFFRACTIONr_nbtor_refined0.3230.52675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5534
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.522
X-RAY DIFFRACTIONr_mcbond_it0.76822426
X-RAY DIFFRACTIONr_mcangle_it1.28533784
X-RAY DIFFRACTIONr_scbond_it0.70321702
X-RAY DIFFRACTIONr_scangle_it0.93631543
LS refinement shellResolution: 2.3→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 181 -
Rwork0.239 3219 -
all-3400 -
obs--88.73 %

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