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- PDB-8j66: Crystal structure of glycosyltransferase SgUGT94-289-3 in complex... -

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Basic information

Entry
Database: PDB / ID: 8j66
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with M3, state 2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / mogroside / UGT / biosynthesis
Function / homology: / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLi, M. / Zhang, S. / Cui, S.
Funding support China, United Kingdom, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)U20A2004 China
Chinese Academy of Sciences#YSBR-015 China
CAMS Innovation Fund for Medical Sciences (CIFMS)2021-I2M-1-071 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the catalytic selectivity of glycosyltransferase SgUGT94-289-3 towards mogrosides.
Authors: Cui, S. / Zhang, S. / Wang, N. / Su, X. / Luo, Z. / Ma, X. / Li, M.
History
DepositionApr 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9394
Polymers51,6091
Non-polymers2,3303
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-9 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.068, 78.127, 94.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycosyltransferase


Mass: 51608.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-M2Q / (2S,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2R,3S,4S,5R,6S)-6-[(3R,6S)-6-[(3S,8S,9R,10R,11S,13R,14S,17S)-3-[(2R,3R,4S,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,4,9,13,14-pentamethyl-11-oxidanyl-2,3,7,8,10,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methyl-2-oxidanyl-heptan-3-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methoxy]oxane-3,4,5-triol


Mass: 963.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H82O19 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium iodide, 20% w/v Polyethylene glycol 3,350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.27→47.33 Å / Num. obs: 24762 / % possible obs: 98.06 % / Redundancy: 4.7 % / Biso Wilson estimate: 27.14 Å2 / CC1/2: 0.986 / Net I/σ(I): 11.23
Reflection shellResolution: 2.275→2.356 Å / Num. unique obs: 2392 / CC1/2: 0.504

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→47.33 Å / SU ML: 0.3486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 1225 4.96 %
Rwork0.2067 23486 -
obs0.2081 24711 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.02 Å2
Refinement stepCycle: LAST / Resolution: 2.27→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 159 187 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00953741
X-RAY DIFFRACTIONf_angle_d1.3825122
X-RAY DIFFRACTIONf_chiral_restr0.2303582
X-RAY DIFFRACTIONf_plane_restr0.0061620
X-RAY DIFFRACTIONf_dihedral_angle_d16.29581309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.370.40021330.31662544X-RAY DIFFRACTION96.61
2.37-2.470.29931300.29342550X-RAY DIFFRACTION97.92
2.47-2.60.28391230.25812564X-RAY DIFFRACTION97.67
2.6-2.770.2571360.24882600X-RAY DIFFRACTION98.84
2.77-2.980.25491320.24132606X-RAY DIFFRACTION98.49
2.98-3.280.27241550.21212581X-RAY DIFFRACTION98.17
3.28-3.750.21021210.17852630X-RAY DIFFRACTION98.29
3.75-4.730.18521480.1562653X-RAY DIFFRACTION98.8
4.73-47.330.17611470.16992758X-RAY DIFFRACTION97.84

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