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

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Basic information

Entry
Database: PDB / ID: 8hjf
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with M5, state 2
Componentsglycosyltransferase
KeywordsTRANSFERASE / mogroside / UGT / Siraitia grosvenorii
Function / homology: / Chem-POG / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (monk fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltransferase
B: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,72210
Polymers103,2462
Non-polymers4,4778
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-9 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.955, 76.814, 81.459
Angle α, β, γ (deg.)90.000, 93.246, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glycosyltransferase


Mass: 51622.820 Da / Num. of mol.: 2 / Mutation: G152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (monk fruit) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 640 molecules

#2: Chemical ChemComp-M1K / (2S,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2R,3S,4S,5R,6R)-6-[[(3S,8S,9R,10R,11R,13R,14S,17R)-17-[(2S,5R)-5-[(2S,3R,4S,5S,6R)-3-[(2R,3R,4S,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[[(2R,3R,4S,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-6-oxidanyl-heptan-2-yl]-4,4,9,13,14-pentamethyl-11-oxidanyl-2,3,7,8,10,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methoxy]oxane-3,4,5-triol


Mass: 1287.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C60H102O29 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 2 / Source method: obtained synthetically / Formula: C21H44O8
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.13 %
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: BL18U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→19.66 Å / Num. obs: 64729 / % possible obs: 99.62 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.88 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 6412 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Blu-Icedata collection
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTD

6jtd


Resolution: 2→19.66 Å / SU ML: 0.2737 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 3426 5.29 %
Rwork0.198 61302 -
obs0.1996 64705 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.89 Å2
Refinement stepCycle: LAST / Resolution: 2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 278 632 7723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527301
X-RAY DIFFRACTIONf_angle_d0.97249946
X-RAY DIFFRACTIONf_chiral_restr0.20021122
X-RAY DIFFRACTIONf_plane_restr0.00641213
X-RAY DIFFRACTIONf_dihedral_angle_d19.47872575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.39571390.32922505X-RAY DIFFRACTION99.66
2.03-2.060.29151410.30112533X-RAY DIFFRACTION99.48
2.06-2.090.31661240.28852550X-RAY DIFFRACTION99.55
2.09-2.130.33561510.29022519X-RAY DIFFRACTION99.93
2.13-2.160.29031240.2792557X-RAY DIFFRACTION99.55
2.16-2.20.29351540.26512554X-RAY DIFFRACTION99.71
2.2-2.240.3011170.2742544X-RAY DIFFRACTION99.59
2.24-2.290.32881460.25382533X-RAY DIFFRACTION99.63
2.29-2.340.2561440.23182558X-RAY DIFFRACTION99.78
2.34-2.390.26541400.22942554X-RAY DIFFRACTION99.85
2.39-2.450.26881350.21872528X-RAY DIFFRACTION99.78
2.45-2.520.26981310.2142571X-RAY DIFFRACTION99.74
2.52-2.590.26161310.20962554X-RAY DIFFRACTION99.81
2.59-2.680.24151280.20192599X-RAY DIFFRACTION99.85
2.68-2.770.2411440.21122528X-RAY DIFFRACTION99.74
2.77-2.880.26621350.20872555X-RAY DIFFRACTION99.93
2.88-3.010.24341410.19692563X-RAY DIFFRACTION99.96
3.01-3.170.22761470.19152545X-RAY DIFFRACTION99.96
3.17-3.370.23651860.18672539X-RAY DIFFRACTION99.93
3.37-3.630.19891700.17372555X-RAY DIFFRACTION100
3.63-3.990.21411290.15942579X-RAY DIFFRACTION99.96
3.99-4.560.18151750.13422554X-RAY DIFFRACTION99.89
4.56-5.730.1881590.14352575X-RAY DIFFRACTION100
5.73-19.660.2531350.15852650X-RAY DIFFRACTION99.46

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