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

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Basic information

Entry
Database: PDB / ID: 8hjk
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with SIA, state 1
Componentsglycosyltranseferease
KeywordsTRANSFERASE / mogroside / UGT / Siraitia grosvenorii
Function / homology: / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (monk fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2214
Polymers51,5671
Non-polymers2,6553
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-10 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.285, 72.527, 78.409
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: 51566.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (monk fruit) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-M0O / (2S,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2S,3S,4S,5R,6S)-5-[(2S,3R,4S,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(3R,6S)-6-[(3S,8S,9R,10R,11S,13R,14S,17R)-3-[(2S,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-bis(oxidanyl)oxan-2-yl]methoxy]oxane-3,4,5-triol


Mass: 1125.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H92O24 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: TacsimateTM, Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.833→18.61 Å / Num. obs: 47496 / % possible obs: 99.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 27.79 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.01
Reflection shellResolution: 1.833→1.899 Å / Num. unique obs: 4684 / CC1/2: 0.777

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Processing

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

6jtd


Resolution: 1.833→18.61 Å / SU ML: 0.1631 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 4389 4.91 %
Rwork0.1837 84937 -
obs0.1846 47451 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 1.833→18.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 181 322 3924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993754
X-RAY DIFFRACTIONf_angle_d1.47515143
X-RAY DIFFRACTIONf_chiral_restr0.4094586
X-RAY DIFFRACTIONf_plane_restr0.0066618
X-RAY DIFFRACTIONf_dihedral_angle_d22.15721304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.833-1.850.32061450.2822766X-RAY DIFFRACTION94.05
1.85-1.880.27451230.27922735X-RAY DIFFRACTION94.35
1.88-1.90.23411250.25562858X-RAY DIFFRACTION99.27
1.9-1.920.28861330.24892904X-RAY DIFFRACTION99.48
1.92-1.950.26261380.24362893X-RAY DIFFRACTION99.47
1.95-1.970.22081230.23572889X-RAY DIFFRACTION99.47
1.97-20.20851360.22122860X-RAY DIFFRACTION99.57
2-2.030.24361430.22152862X-RAY DIFFRACTION99.5
2.03-2.060.22361600.21552913X-RAY DIFFRACTION99.58
2.06-2.10.21931340.21542853X-RAY DIFFRACTION99.67
2.1-2.130.2291360.20732928X-RAY DIFFRACTION99.55
2.13-2.170.21421260.20152840X-RAY DIFFRACTION99.5
2.17-2.210.19711200.20112914X-RAY DIFFRACTION99.38
2.21-2.260.21851760.1922858X-RAY DIFFRACTION99.41
2.26-2.310.18311950.19842775X-RAY DIFFRACTION98.84
2.31-2.360.18121810.19362822X-RAY DIFFRACTION98.91
2.36-2.420.18731560.1932851X-RAY DIFFRACTION98.43
2.42-2.490.21221410.19872862X-RAY DIFFRACTION98.27
2.49-2.560.22841190.19782848X-RAY DIFFRACTION98.05
2.56-2.640.22031430.19832807X-RAY DIFFRACTION98.07
2.64-2.740.21051610.2012804X-RAY DIFFRACTION97.6
2.74-2.850.24981700.21182790X-RAY DIFFRACTION96.99
2.85-2.970.23081560.19952811X-RAY DIFFRACTION97.57
2.97-3.130.22341320.21042805X-RAY DIFFRACTION96.68
3.13-3.330.20441680.18512785X-RAY DIFFRACTION97.52
3.33-3.580.1791560.16632802X-RAY DIFFRACTION97.46
3.58-3.940.19081490.15622809X-RAY DIFFRACTION96.95
3.94-4.50.15731370.14412752X-RAY DIFFRACTION96.24
4.5-5.650.18861680.14452768X-RAY DIFFRACTION96.07
5.65-18.610.16351390.15062773X-RAY DIFFRACTION96.3

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