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

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Basic information

Entry
Database: PDB / ID: 8hjp
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with UDP state 1
Componentsglycosyltranseferease
KeywordsTRANSFERASE / mogroside / UGT / Siraitia grosvenorii
Function / homologyChem-POG / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (monk fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionNov 23, 2022Deposition 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltranseferease
B: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4505
Polymers103,2182
Non-polymers1,2333
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-9 kcal/mol
Surface area19830 Å2
MethodPISA
2
A: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4383
Polymers51,6091
Non-polymers8292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-9 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.742, 80.873, 173.379
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 glycosyltranseferease


Mass: 51608.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (monk fruit) / Production host: Escherichia coli (E. coli) / References: Transferases
#2: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl, polyethylene glycol 3350, NaCl, Polypropylene glycol P400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→35.84 Å / Num. obs: 46304 / % possible obs: 99.65 % / Redundancy: 12.8 % / Biso Wilson estimate: 30.48 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.91
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 4553 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTD

6jtd


Resolution: 2.2→35.84 Å / SU ML: 0.2836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 2370 5.13 %
Rwork0.2285 43815 -
obs0.2301 46185 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 71 322 7180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00587084
X-RAY DIFFRACTIONf_angle_d0.99889619
X-RAY DIFFRACTIONf_chiral_restr0.06291050
X-RAY DIFFRACTIONf_plane_restr0.00531218
X-RAY DIFFRACTIONf_dihedral_angle_d20.26582555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.36421460.29182518X-RAY DIFFRACTION99.78
2.24-2.290.34641370.29172540X-RAY DIFFRACTION100
2.29-2.350.32141370.27452543X-RAY DIFFRACTION99.74
2.35-2.410.31441280.27692538X-RAY DIFFRACTION99.63
2.41-2.470.32781280.26532560X-RAY DIFFRACTION99.81
2.47-2.540.3161370.26132546X-RAY DIFFRACTION99.63
2.54-2.630.28051290.25232568X-RAY DIFFRACTION99.81
2.63-2.720.33071460.27082553X-RAY DIFFRACTION99.82
2.72-2.830.30561350.27082534X-RAY DIFFRACTION99.66
2.83-2.960.3051470.25812571X-RAY DIFFRACTION99.67
2.96-3.110.28331380.24962590X-RAY DIFFRACTION99.96
3.11-3.310.29871340.24572574X-RAY DIFFRACTION99.85
3.31-3.560.21611400.22962592X-RAY DIFFRACTION99.82
3.56-3.920.2411350.20972599X-RAY DIFFRACTION99.78
3.92-4.490.22121360.18682633X-RAY DIFFRACTION99.68
4.49-5.650.22341600.18312616X-RAY DIFFRACTION99.57
5.65-35.840.18111570.19232740X-RAY DIFFRACTION98.5

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