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- PDB-2bfw: Structure of the C domain of glycogen synthase from Pyrococcus abyssi -

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Basic information

Entry
Database: PDB / ID: 2bfw
TitleStructure of the C domain of glycogen synthase from Pyrococcus abyssi
ComponentsGLGA GLYCOGEN SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE FAMILY 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE TWO ROSSMAN FOLDS
Function / homology
Function and homology information


alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity
Similarity search - Function
Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glycogen synthase
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHorcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of an Archaeal Glycogen Synthase: Insights Into Oligomerisation and Substrate Binding of Eukaryotic Glycogen Synthases.
Authors: Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
History
DepositionDec 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLGA GLYCOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7547
Polymers22,2521
Non-polymers5026
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.614, 50.820, 44.261
Angle α, β, γ (deg.)90.00, 106.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLGA GLYCOGEN SYNTHASE / C DOMAIN OF GLYCOGEN SYNTHASE


Mass: 22251.660 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 218-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.9 Å3/Da / Density % sol: 36.1 %
Crystal growpH: 4.6
Details: 30% PEG8K, 0.1 M NAAC PH 4.5, 0.2M LITHIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.9
DetectorType: MARRESEAERCH / Detector: CCD / Date: Nov 12, 2004 / Details: FLAT MIRROR AND A TOROIDAL MIRROR
RadiationMonochromator: 2 CRYSTALS MONOCROMATOR. SI(111). 140-X-80 X 20 MM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 1.8→37.9 Å / Num. obs: 15701 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.5 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZU

1rzu


Resolution: 1.8→42.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.002 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 744 4.9 %RANDOM
Rwork0.183 ---
obs0.186 14581 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.09 Å2
2--0.07 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 28 169 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9932347
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74523.47272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6421514
X-RAY DIFFRACTIONr_chiral_restr0.070.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021311
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2862
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.51107
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91421738
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3963698
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2374.5609
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 58
Rwork0.256 833
Refinement TLS params.Method: refined / Origin x: -3.2048 Å / Origin y: -0.1211 Å / Origin z: 10.5415 Å
111213212223313233
T-0.0142 Å20.0008 Å20.0029 Å2--0.0236 Å20 Å2---0.0224 Å2
L0.7587 °2-0.0999 °20.1608 °2-0.3786 °2-0.1899 °2--0.4552 °2
S0.0178 Å °0.0207 Å °0.0079 Å °-0.0354 Å °0.0036 Å °0.0016 Å °0.0397 Å °0.0094 Å °-0.0214 Å °

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