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- PDB-3d1j: Crystal Structure of E.coli GS mutant dmGS(C7S;C408S) -

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Basic information

Entry
Database: PDB / ID: 3d1j
TitleCrystal Structure of E.coli GS mutant dmGS(C7S;C408S)
ComponentsGlycogen synthase
KeywordsTRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / open form / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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
DepositionMay 6, 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 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 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


Theoretical massNumber of molelcules
Total (without water)52,8481
Polymers52,8481
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)232.959, 232.959, 85.539
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 52848.078 Da / Num. of mol.: 1 / Mutation: C7S, C408S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% (w/v) PEG 4000, 0.1 M Tris, 0.2 M Na tartrate, 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: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 21907 / Num. obs: 20539 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.3
Reflection shellResolution: 3→3.15 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2 / Num. unique all: 2180 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.54 / Cor.coef. Fo:Fc: 0.485
Highest resolutionLowest resolution
Rotation3 Å31.41 Å
Translation3 Å31.41 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZU

1rzu


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.38 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.909 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 879 5 %RANDOM
Rwork0.209 ---
all0.249 ---
obs0.212 17683 99.08 %-
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: 50.651 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.64 Å20 Å2
2--1.29 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 0 20 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223818
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.955194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30922.849179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34915587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6821530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022973
X-RAY DIFFRACTIONr_nbd_refined0.2840.32036
X-RAY DIFFRACTIONr_nbtor_refined0.3460.52639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.58
X-RAY DIFFRACTIONr_mcbond_it0.88222381
X-RAY DIFFRACTIONr_mcangle_it1.54633758
X-RAY DIFFRACTIONr_scbond_it0.68121612
X-RAY DIFFRACTIONr_scangle_it1.07631435
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 65 -
Rwork0.285 1234 -
all-1299 -
obs--99.85 %

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