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- PDB-8zi6: Crystal structure of SrUGT76G4 in complex with UDP-glucose -

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Basic information

Entry
Database: PDB / ID: 8zi6
TitleCrystal structure of SrUGT76G4 in complex with UDP-glucose
ComponentsUGT-glycosyltransferase 76G4
KeywordsTRANSFERASE / Glycosyltransferase / Steviol glycosides / UDP-glucose / Complex
Function / homologyISOPROPYL ALCOHOL / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE
Function and homology information
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, Y. / Li, T. / Yin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Functional Characterization and Structural Insights into SrUGT76G1-4 from Stevia Rebaudioside Reveal a Residue Critical for the Regioselectivity and efficient Rebaudioside M synthesis
Authors: Wang, Y. / Li, T. / Yin, H.
History
DepositionMay 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UGT-glycosyltransferase 76G4
B: UGT-glycosyltransferase 76G4
C: UGT-glycosyltransferase 76G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7927
Polymers156,5043
Non-polymers1,2884
Water181
1
A: UGT-glycosyltransferase 76G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7943
Polymers52,1681
Non-polymers6262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-6 kcal/mol
Surface area18990 Å2
MethodPISA
2
B: UGT-glycosyltransferase 76G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7342
Polymers52,1681
Non-polymers5661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-7 kcal/mol
Surface area17580 Å2
MethodPISA
3
C: UGT-glycosyltransferase 76G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2632
Polymers52,1681
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-7 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.780, 111.780, 91.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein UGT-glycosyltransferase 76G4


Mass: 52168.031 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Production host: Escherichia coli (E. coli)
References: Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.2 M NaSCN, 0.1 M NaCitrate pH5.5, 10-35% PEG3350, 8% D-Sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→33.99 Å / Num. obs: 30343 / % possible obs: 96.1 % / Redundancy: 6.9 % / CC1/2: 0.971 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.094 / Rrim(I) all: 0.267 / Net I/σ(I): 5.4 / Num. measured all: 209055
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 86.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.912 / Num. measured all: 20469 / Num. unique obs: 4019 / CC1/2: 0.554 / Rpim(I) all: 0.397 / Rrim(I) all: 1.003 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALA3.3.22data scaling
MOSFLM7.4.0data reduction
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→33.99 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.773 / SU B: 28.225 / SU ML: 0.57 / Cross valid method: THROUGHOUT / ESU R Free: 0.581 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35122 1560 5.1 %RANDOM
Rwork0.26806 ---
obs0.27244 28750 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å2-0 Å2
2--0.27 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.8→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9354 0 59 1 9414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129655
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169049
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.81913106
X-RAY DIFFRACTIONr_angle_other_deg0.4591.74520841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.47751161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.362557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.263101617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022263
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6755.5144674
X-RAY DIFFRACTIONr_mcbond_other3.6755.5144674
X-RAY DIFFRACTIONr_mcangle_it6.049.95819
X-RAY DIFFRACTIONr_mcangle_other6.0399.95820
X-RAY DIFFRACTIONr_scbond_it3.1015.7594981
X-RAY DIFFRACTIONr_scbond_other3.15.7584978
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.23410.5017280
X-RAY DIFFRACTIONr_long_range_B_refined9.16553.2111262
X-RAY DIFFRACTIONr_long_range_B_other9.16453.2111263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 97 -
Rwork0.317 1860 -
obs--83.67 %

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