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- PDB-8zi7: Crystal structure of SrUGT76G4 in complex with Rubusoside -

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Basic information

Entry
Database: PDB / ID: 8zi7
TitleCrystal structure of SrUGT76G4 in complex with Rubusoside
ComponentsUGT-glycosyltransferase 76G4
KeywordsTRANSFERASE / Glycosyltransferase / Steviol glycosides / Rubusoside / Complex
Function / homologyChem-AQ9 / ETHANOL / ISOPROPYL ALCOHOL / THIOCYANATE ION
Function and homology information
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: UGT-glycosyltransferase 76G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1649
Polymers52,1681
Non-polymers9968
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-4 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.026, 77.228, 86.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UGT-glycosyltransferase 76G4


Mass: 52168.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 7 types, 82 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AQ9 / 1-O-[(8alpha,9beta,10alpha,13alpha)-13-(beta-D-glucopyranosyloxy)-18-oxokaur-16-en-18-yl]-beta-D-glucopyranose / Rubusoside


Mass: 642.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C32H50O13 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.88 %
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: 0.97914 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.1→57.5 Å / Num. obs: 28050 / % possible obs: 95.7 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 0.88 / Net I/σ(I): 12 / Num. measured all: 180199
Reflection shellResolution: 2.1→2.22 Å / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.927 / Num. measured all: 28943 / Num. unique obs: 4198 / CC1/2: 0.756 / Rpim(I) all: 0.369 / Rrim(I) all: 1.001 / Χ2: 0.68 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimless0.7.7data scaling
autoPROC1.0.5data reduction
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→57.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.866 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1385 4.9 %RANDOM
Rwork0.1827 ---
obs0.1853 26602 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.002 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---0.36 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.1→57.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 66 74 3378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163231
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.8224654
X-RAY DIFFRACTIONr_angle_other_deg0.5651.7497449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0035412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.862525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23710575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02813
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_it4.4475.1141623
X-RAY DIFFRACTIONr_mcbond_other4.4395.1131621
X-RAY DIFFRACTIONr_mcangle_it6.329.1762024
X-RAY DIFFRACTIONr_mcangle_other6.3229.1762025
X-RAY DIFFRACTIONr_scbond_it5.6615.8151801
X-RAY DIFFRACTIONr_scbond_other5.6595.8151802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.76810.3442625
X-RAY DIFFRACTIONr_long_range_B_refined11.37252.913815
X-RAY DIFFRACTIONr_long_range_B_other11.37452.923813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.105→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 91 -
Rwork0.279 2016 -
obs--99.53 %

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