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- PDB-7fga: Alpha-1,2-glucosyltransferase_UDP_sucrose_tll1591 -

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Basic information

Entry
Database: PDB / ID: 7fga
TitleAlpha-1,2-glucosyltransferase_UDP_sucrose_tll1591
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / alpha-1 / 2-glucosyltransferase_UDP_sucrose_tll1591
Function / homologyGlycosyl transferase 4-like domain / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / surcrose isoform / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSu, J.Y.
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2022
Title: Structural basis for glucosylsucrose synthesis by a member of the alpha-1,2-glucosyltransferase family
Authors: Han, Q. / Yao, Y. / Liu, Y. / Zhang, W. / Yu, J. / Na, H. / Liu, T. / Mayo, K. / Su, J.
History
DepositionJul 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
B: Glycosyl transferase
C: Glycosyl transferase
D: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,61812
Polymers161,6324
Non-polymers2,9868
Water00
1
A: Glycosyl transferase
hetero molecules

B: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3096
Polymers80,8162
Non-polymers1,4934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area4390 Å2
ΔGint-30 kcal/mol
Surface area27750 Å2
MethodPISA
2
C: Glycosyl transferase
hetero molecules

D: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3096
Polymers80,8162
Non-polymers1,4934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444x-y-1,x-1,z-1/61
Buried area4550 Å2
ΔGint-28 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.712, 157.712, 187.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Glycosyl transferase


Mass: 40407.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll1591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIJ4
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: surcrose isoform
DescriptorTypeProgram
DGlcpa1-1DFrufa2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2a_2-5][a2122h-1a_1-5]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-L-Fruf]{}LINUCSPDB-CARE
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY

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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: 4.17 Å3/Da / Density % sol: 70.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→19.96 Å / Num. obs: 43413 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 6364

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FG9

7fg9


Resolution: 3.2→19.96 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3272 2018 4.65 %
Rwork0.2922 41376 -
obs0.2939 43394 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.89 Å2 / Biso mean: 64.6819 Å2 / Biso min: 28.16 Å2
Refinement stepCycle: final / Resolution: 3.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10872 0 192 0 11064
Biso mean--66.19 --
Num. residues----1376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.280.42321460.372229693115100
3.28-3.370.41161440.369529573101100
3.37-3.470.43581420.359829203062100
3.47-3.580.38491430.35729543097100
3.58-3.70.35961440.333629363080100
3.7-3.850.36911480.333129623110100
3.85-4.030.35051440.31329533097100
4.03-4.240.36061430.305529523095100
4.24-4.50.33051450.283129453090100
4.5-4.840.28791410.268829523093100
4.84-5.320.29841460.273329663112100
5.32-6.070.29671390.280729633102100
6.07-7.580.3021470.272929593106100
7.58-19.960.25291460.2172988313499

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