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- PDB-6kvl: Crystal structure of UDP-RebB-SrUGT76G1 -

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Basic information

Entry
Database: PDB / ID: 6kvl
TitleCrystal structure of UDP-RebB-SrUGT76G1
ComponentsUDP-glycosyltransferase 76G1
KeywordsTRANSFERASE / glycosyltransferase / diterpenoid / Stevia rebaudiana / natural sweeteners / steviol glycosides (SGs).
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AUO / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLi, J.X. / Liu, Z.F. / Wang, Y. / Zhang, P.
Funding support China, 8items
OrganizationGrant numberCountry
National Natural Science Foundation of China2018YFA0900600 China
Chinese Academy of SciencesXDB27020202 China
Chinese Academy of SciencesXDB27020103 China
National Natural Science Foundation of China31700261 China
National Natural Science Foundation of China31700263 China
National Natural Science Foundation of China31670099 China
Chinese Academy of SciencesZSYS-016 China
Chinese Academy of Sciences153D31KYSB20170121 China
CitationJournal: Plant Commun. / Year: 2020
Title: Structural Insights into the Catalytic Mechanism of a Plant Diterpene Glycosyltransferase SrUGT76G1.
Authors: Liu, Z. / Li, J. / Sun, Y. / Zhang, P. / Wang, Y.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6153
Polymers52,4061
Non-polymers1,2092
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.463, 97.463, 89.899
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

21A-842-

HOH

31A-926-

HOH

41A-927-

HOH

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Components

#1: Protein UDP-glycosyltransferase 76G1


Mass: 52406.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-AUO / (8alpha,9beta,10alpha,13alpha)-13-{[beta-D-glucopyranosyl-(1->2)-[beta-D-glucopyranosyl-(1->3)]-beta-D-glucopyranosyl]oxy}kaur-16-en-18-oic acid


Mass: 804.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H60O18 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% (vol/vol) 2-propanol, 0.1M sodium citrate tribasic dihydrate, pH 5.5, 18% (wt/vol) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.998→39.674 Å / Num. obs: 53258 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.994 / Rrim(I) all: 0.153 / Net I/σ(I): 26.6
Reflection shellResolution: 1.998→2.07 Å / Num. unique obs: 3321 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCE

2vce


Resolution: 1.998→39.674 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 2700 5.07 %
Rwork0.1676 50558 -
obs0.1695 53258 82.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.75 Å2 / Biso mean: 31.6381 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: final / Resolution: 1.998→39.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 151 328 4057
Biso mean--20.83 35.38 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013755
X-RAY DIFFRACTIONf_angle_d1.4035115
X-RAY DIFFRACTIONf_chiral_restr0.106571
X-RAY DIFFRACTIONf_plane_restr0.006644
X-RAY DIFFRACTIONf_dihedral_angle_d23.2391362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9982-2.03460.2513880.2361164450
2.0346-2.07370.2679900.2228166452
2.0737-2.1160.2279840.2119168752
2.116-2.1620.2514910.2031172254
2.162-2.21230.2326990.2025188657
2.2123-2.26770.21951140.1903199562
2.2677-2.3290.22841320.1917230871
2.329-2.39750.2651340.1904263883
2.3975-2.47490.22041600.1861292991
2.4749-2.56330.24291640.1833314396
2.5633-2.66590.2211690.1861316898
2.6659-2.78720.23231680.1739319399
2.7872-2.93410.20411690.1762322099
2.9341-3.11790.19961720.17673220100
3.1179-3.35850.19831720.16963254100
3.3585-3.69620.21821720.1533224100
3.6962-4.23060.16191780.14183211100
4.2306-5.3280.17351710.14063236100
5.328-39.6740.19181730.1558321699

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