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- PDB-3fro: Crystal structure of Pyrococcus abyssi glycogen synthase with ope... -

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Basic information

Entry
Database: PDB / ID: 3fro
TitleCrystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations
ComponentsGlgA glycogen synthase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE FAMILY / UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE / TWO ROSSMAN FOLDS
Function / homology
Function and homology information


glycogen (starch) synthase activity / glycogen biosynthetic process / cytosol
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
1,5-anhydro-D-fructose / PHOSPHATE ION / Glycogen synthase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsDiaz, A. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
CitationJournal: IUBMB Life / Year: 2012
Title: Lyase activity of glycogen synthase: Is an elimination/addition mechanism a possible reaction pathway for retaining glycosyltransferases?
Authors: Diaz, A. / Diaz-Lobo, M. / Grados, E. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations
Category: struct_ref_seq_dif / struct_site / struct_site_gen
Item: _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GlgA glycogen synthase
B: GlgA glycogen synthase
C: GlgA glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,83810
Polymers148,0253
Non-polymers8137
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area52030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.998, 139.913, 159.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GlgA glycogen synthase


Mass: 49341.617 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)/pG-Tf2
References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-NHF / 1,5-anhydro-D-fructose


Type: D-saccharide / Mass: 162.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 26-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 58723 / Num. obs: 58364 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.099 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1964 / Rsym value: 0.32 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementStarting model: PDB ENTRY 2BIS

2bis


Resolution: 2.5→24.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.683 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.496 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2950 5.1 %RANDOM
Rwork0.214 ---
all0.288 58527 --
obs0.216 58364 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.51 Å2 / Biso mean: 43.416 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.92 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10452 0 50 95 10597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210787
X-RAY DIFFRACTIONr_bond_other_d0.0010.027558
X-RAY DIFFRACTIONr_angle_refined_deg0.8251.96714554
X-RAY DIFFRACTIONr_angle_other_deg0.743.00118276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.80351322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78523.006489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.931151875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8181578
X-RAY DIFFRACTIONr_chiral_restr0.050.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022380
X-RAY DIFFRACTIONr_nbd_refined0.1660.22118
X-RAY DIFFRACTIONr_nbd_other0.1680.27483
X-RAY DIFFRACTIONr_nbtor_refined0.1730.25236
X-RAY DIFFRACTIONr_nbtor_other0.080.25717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1240.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.26
X-RAY DIFFRACTIONr_mcbond_it0.2231.58567
X-RAY DIFFRACTIONr_mcbond_other0.0211.52723
X-RAY DIFFRACTIONr_mcangle_it0.245210484
X-RAY DIFFRACTIONr_scbond_it0.32235074
X-RAY DIFFRACTIONr_scangle_it0.4944.54070
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 210 -
Rwork0.358 3953 -
all-4163 -
obs-1964 98.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46930.04830.37792.1599-0.10341.8617-0.01680.04380.02850.052-0.0428-0.0805-0.02440.04780.0597-0.0903-0.0219-0.0162-0.47450.02280.071452.02485.046-46.752
21.40340.6188-0.20622.0894-0.49871.9486-0.00250.0419-0.0671-0.0976-0.0099-0.0320.0675-0.05260.0124-0.06490.0129-0.0349-0.4544-0.02070.030935.20951.361-46.834
31.83050.720.1993.6971-0.4652.07030.0666-0.20720.08250.5226-0.145-0.0621-0.2815-0.00050.07840.0864-0.0294-0.0488-0.36820.0125-0.004946.47566.626-14.366
43.7401-0.0969-0.74134.68050.06441.58210.13030.046-0.02860.0272-0.0063-0.2601-0.03360.2478-0.1239-0.0211-0.0642-0.094-0.2789-0.03250.121575.571108.538-36.574
55.64720.07332.56473.88340.73243.46360.05350.8-0.9854-0.5660.02560.18070.27260.133-0.07910.3241-0.0330.0492-0.0659-0.24990.40434.59442.037-77.126
63.2610.1729-0.60982.0499-0.76894.0058-0.0971-0.1255-0.025-0.07750.0814-0.04070.2924-0.11170.01560.0423-0.0448-0.0344-0.4066-0.01420.083340.91639.6976.188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 217
2X-RAY DIFFRACTION1A414 - 437
3X-RAY DIFFRACTION2B0 - 217
4X-RAY DIFFRACTION2B414 - 437
5X-RAY DIFFRACTION3C0 - 217
6X-RAY DIFFRACTION3C414 - 437
7X-RAY DIFFRACTION4A218 - 413
8X-RAY DIFFRACTION5B218 - 413
9X-RAY DIFFRACTION6C218 - 413

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