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- PDB-8hjq: Crystal structure of glycosyltransferase SgUGT94-289-3 in apo state -

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Basic information

Entry
Database: PDB / ID: 8hjq
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in apo state
Componentsglycosyltranseferease
KeywordsTRANSFERASE / mogroside / UGT / siraitia grosvenorii
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltranseferease


Theoretical massNumber of molelcules
Total (without water)51,6091
Polymers51,6091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19690 Å2
Unit cell
Length a, b, c (Å)63.901, 81.433, 90.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein glycosyltranseferease


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) / References: Transferases
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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting 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: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.05→60.41 Å / Num. obs: 9376 / % possible obs: 99.63 % / Redundancy: 6.1 % / Biso Wilson estimate: 75.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1095 / Net I/σ(I): 13.23
Reflection shellResolution: 3.05→3.159 Å / Num. unique obs: 900 / CC1/2: 0.845

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Processing

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

6jtd


Resolution: 3.05→60.41 Å / SU ML: 0.3411 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 855 4.96 %
Rwork0.2219 16379 -
obs0.2237 9366 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.15 Å2
Refinement stepCycle: LAST / Resolution: 3.05→60.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 0 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063231
X-RAY DIFFRACTIONf_angle_d1.28884400
X-RAY DIFFRACTIONf_chiral_restr0.0725489
X-RAY DIFFRACTIONf_plane_restr0.0099563
X-RAY DIFFRACTIONf_dihedral_angle_d14.11041133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.240.38651260.31412721X-RAY DIFFRACTION99.82
3.24-3.490.29351500.24762720X-RAY DIFFRACTION100
3.49-3.840.28851520.25842730X-RAY DIFFRACTION99.97
3.84-4.40.23691490.21312725X-RAY DIFFRACTION99.55
4.4-5.540.21631530.20082725X-RAY DIFFRACTION99.62
5.54-60.410.25581250.1972758X-RAY DIFFRACTION99.31

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