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

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Basic information

Entry
Database: PDB / ID: 8hjo
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with UDP state 2
Componentsglycosyltranseferease
KeywordsTRANSFERASE / mogroside / UGT / Siraitia grosvenorii
Function / homologyDI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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: glycosyltranseferease
B: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1007
Polymers102,9412
Non-polymers1,1595
Water10,683593
1
A: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9973
Polymers51,4711
Non-polymers5262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-9 kcal/mol
Surface area18810 Å2
MethodPISA
2
B: glycosyltranseferease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1034
Polymers51,4711
Non-polymers6323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-9 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.159, 78.270, 96.625
Angle α, β, γ (deg.)90.000, 92.925, 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

#1: Protein glycosyltranseferease


Mass: 51470.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Production host: Escherichia coli (E. coli) / References: Transferases
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
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: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.64→24.12 Å / Num. obs: 96842 / % possible obs: 91.37 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.52 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.46
Reflection shellResolution: 1.64→1.699 Å / Num. unique obs: 70398 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Blu-Ice1.18.2_3874data collection
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTD

6jtd


Resolution: 1.64→24.12 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 9127 4.81 %
Rwork0.1667 180491 -
obs0.168 96793 91.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.03 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6949 0 73 593 7615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067257
X-RAY DIFFRACTIONf_angle_d0.8429850
X-RAY DIFFRACTIONf_chiral_restr0.05521064
X-RAY DIFFRACTIONf_plane_restr0.00611252
X-RAY DIFFRACTIONf_dihedral_angle_d22.9412646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.30492930.25386671X-RAY DIFFRACTION99.77
1.66-1.680.28842990.25026555X-RAY DIFFRACTION99.84
1.68-1.70.24883530.22796649X-RAY DIFFRACTION99.87
1.7-1.720.26993740.21886652X-RAY DIFFRACTION99.8
1.72-1.740.27113530.21856496X-RAY DIFFRACTION99.9
1.74-1.770.2733310.21296678X-RAY DIFFRACTION99.8
1.77-1.790.23423380.20546520X-RAY DIFFRACTION99.9
1.79-1.820.24193320.20076674X-RAY DIFFRACTION99.97
1.82-1.850.24493090.19676578X-RAY DIFFRACTION99.83
1.85-1.880.25872360.20144854X-RAY DIFFRACTION87.13
1.88-1.910.25291330.20962775X-RAY DIFFRACTION93.21
1.91-1.940.27661430.21062887X-RAY DIFFRACTION46.85
1.94-1.980.22431510.18662846X-RAY DIFFRACTION97.27
1.98-2.020.21543380.18366629X-RAY DIFFRACTION99.93
2.02-2.070.21143670.18426585X-RAY DIFFRACTION99.56
2.07-2.110.22183100.17576637X-RAY DIFFRACTION99.77
2.11-2.170.19093460.17856599X-RAY DIFFRACTION99.88
2.17-2.230.22713100.17156624X-RAY DIFFRACTION99.78
2.23-2.290.19562060.17753583X-RAY DIFFRACTION54.79
2.29-2.370.2072960.17186634X-RAY DIFFRACTION99.93
2.37-2.450.19713310.16966653X-RAY DIFFRACTION99.86
2.45-2.550.19643430.16786584X-RAY DIFFRACTION99.87
2.55-2.660.21353010.17036607X-RAY DIFFRACTION99.75
2.66-2.80.23063760.1766544X-RAY DIFFRACTION99.68
2.8-2.980.19813070.17946607X-RAY DIFFRACTION99.1
2.98-3.210.20693750.17036590X-RAY DIFFRACTION99.81
3.21-3.530.16693350.1536571X-RAY DIFFRACTION99.77
3.53-4.040.15662920.13815094X-RAY DIFFRACTION77.72
4.04-5.090.12983460.12756610X-RAY DIFFRACTION99.66
5.09-24.120.18353030.15416505X-RAY DIFFRACTION97.87

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