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

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Basic information

Entry
Database: PDB / ID: 8hjl
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with M3E
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / mogroside / UGT / biosynthesis
Function / homology: / Chem-POG / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,82114
Polymers103,2182
Non-polymers6,60312
Water22,5191250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-11 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.633, 76.161, 82.254
Angle α, β, γ (deg.)90.000, 92.590, 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: 51608.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Gene: LOC111022978 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 1262 molecules

#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: 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
#4: 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.: 4 / Source method: obtained synthetically / Formula: C21H44O8
#5: Chemical
ChemComp-M7F / (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(3S,8S,9R,10S,11S,13R,14S,17S)-17-[(2S,5R)-5-[(2S,3R,4S,5R,6S)-6-(hydroxymethyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-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]oxane-3,4,5-triol


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


Mass: 18.015 Da / Num. of mol.: 1250 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
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: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 101044 / % possible obs: 90.88 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.55
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 5425 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
AutoProcessdata processing
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTD

6jtd


Resolution: 1.72→24.63 Å / SU ML: 0.2147 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 4757 4.71 %
Rwork0.2104 96286 -
obs0.2125 101043 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.05 Å2
Refinement stepCycle: LAST / Resolution: 1.72→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6810 0 438 1250 8498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00677528
X-RAY DIFFRACTIONf_angle_d1.079410280
X-RAY DIFFRACTIONf_chiral_restr0.36821177
X-RAY DIFFRACTIONf_plane_restr0.00731225
X-RAY DIFFRACTIONf_dihedral_angle_d14.93332659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.30111280.24562683X-RAY DIFFRACTION82.17
1.74-1.760.2641510.23693220X-RAY DIFFRACTION98.94
1.76-1.780.28091700.21813240X-RAY DIFFRACTION98.9
1.78-1.80.29921420.21853239X-RAY DIFFRACTION98.92
1.8-1.820.2671590.223280X-RAY DIFFRACTION98.94
1.82-1.850.25561700.22183216X-RAY DIFFRACTION99.15
1.85-1.880.28711610.23823230X-RAY DIFFRACTION99.12
1.88-1.90.3271920.27223212X-RAY DIFFRACTION98.78
1.9-1.930.41831540.35512866X-RAY DIFFRACTION88.9
1.93-1.970.3091460.25053308X-RAY DIFFRACTION99.34
1.97-20.28331650.22823229X-RAY DIFFRACTION99.44
2-2.040.29351760.22553252X-RAY DIFFRACTION99.65
2.04-2.070.3231490.27773084X-RAY DIFFRACTION93.82
2.07-2.120.25051760.21723259X-RAY DIFFRACTION99.19
2.12-2.160.28411720.21013234X-RAY DIFFRACTION99.65
2.16-2.210.26781700.21013233X-RAY DIFFRACTION99.65
2.21-2.270.32711360.26632979X-RAY DIFFRACTION90.47
2.27-2.330.25041660.2263291X-RAY DIFFRACTION99.54
2.33-2.40.26411680.20843247X-RAY DIFFRACTION99.74
2.4-2.480.28051480.20563299X-RAY DIFFRACTION99.86
2.48-2.560.25081600.21083265X-RAY DIFFRACTION99.8
2.56-2.670.24421480.20693310X-RAY DIFFRACTION99.68
2.67-2.790.2411370.20583294X-RAY DIFFRACTION99.59
2.79-2.930.22551750.19963282X-RAY DIFFRACTION99.65
2.93-3.120.2221860.19363250X-RAY DIFFRACTION99.57
3.12-3.360.22791280.18663292X-RAY DIFFRACTION99.1
3.36-3.70.23611160.17733273X-RAY DIFFRACTION97.72
3.7-4.230.20791270.17163228X-RAY DIFFRACTION96.05
4.23-5.320.19942140.17073212X-RAY DIFFRACTION97.91
5.32-24.630.23561670.19873279X-RAY DIFFRACTION96.77

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