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- PDB-7fg9: Alpha-1,2-glucosyltransferase_UDP_tll1591 -

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Basic information

Entry
Database: PDB / ID: 7fg9
TitleAlpha-1,2-glucosyltransferase_UDP_tll1591
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / alapha-1 / 2-glucosyltransferase_UDP_tll1591
Function / homology
Function and homology information


biosynthetic process / glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyl transferase 4-like domain / : / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6244
Polymers80,8162
Non-polymers8082
Water1,15364
1
A: Glycosyl transferase
hetero molecules

B: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6244
Polymers80,8162
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/21
Buried area2230 Å2
ΔGint-15 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.643, 177.643, 57.034
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Glycosyl transferase


Mass: 40407.930 Da / Num. of mol.: 2
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.66→19.23 Å / Num. obs: 28981 / % possible obs: 98.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 2.66→2.79 Å / Rmerge(I) obs: 0.505 / Num. unique obs: 3875

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OY2

3oy2


Resolution: 2.66→19.23 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1992 6.88 %
Rwork0.1785 26973 -
obs0.1819 28965 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.58 Å2 / Biso mean: 51.0501 Å2 / Biso min: 27.73 Å2
Refinement stepCycle: final / Resolution: 2.66→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5394 0 50 64 5508
Biso mean--44.21 48.15 -
Num. residues----682
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 (%)
2.66-2.730.30461410.25771940208199
2.73-2.80.33581430.241917206099
2.8-2.880.28061430.23091950209398
2.88-2.970.31051430.21911941208498
2.97-3.080.2471410.20661914205598
3.08-3.20.25721480.20941945209398
3.2-3.350.27221420.19451922206497
3.35-3.520.24551380.18121931206997
3.52-3.740.2541450.17221902204797
3.74-4.030.22941460.17591921206797
4.03-4.430.20241360.15141924206096
4.43-5.060.18751410.1441911205296
5.06-6.340.20051400.18371944208496
6.34-19.230.17581450.15791911205693

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